KISMAYU, Somalia, Dec. 28— More than 100 religious leaders and business executives, a doctor and other prominent residents of this port city were hunted door to door and killed in three nights of terror that began on the eve of the American landing in Mogadishu, Somali witnesses and United States diplomats say.

The killings were directed by the clan leader who controls Kismayu in a move to eliminate educated Somalis who might support the Americans, United States officials in Somalia said in interviews over the past two days. All the victims were Harti, who have deep roots here and say they regard other clans as occupiers.

The clan leader was identified as Col. Omar Jess, a member of the Ogadeni clan, who seized control of the city in May. Recent public statements by him seem to support the assessment of the United States officials, who are directing more than 20,000 troops in securing relief supplies for this famine- and war-wracked country. The Night the Trucks Rolled

The night the killings began, trucks roared through town and wild gunshots could be heard as Harti were pulled from their homes and killed on the edge of the town, Somali witnesses said.

The killing is continuing, but sporadically, Somalis say, adding that the timing and the circumstances of the massacre show the treacherous terrain of clan politics that the Americans are stepping into in Somalia.

Colonel Jess, who has tried to ingratiate himself with the Americans, apparently used their impending arrival as an excuse to wipe out rivals, one associate said. On Dec. 19, 11 days after the first killings, Colonel Jess warmly welcomed President Bush’s special envoy to Somalia, Robert B. Oakley. The next day American troops arrived in Kismayu. A Roundup at 3 A.M.

The colonel also has a strong ally in Gen. Mohammed Farah Aidid, one of the two clan leaders who control Mogadishu and who have been the focus of Western diplomatic efforts.

[ General Aidid and his rival, Mohammed Ali Mahdi, embraced publicly in Mogadishu, renewing promises to end hostilities. Page A6. ]

Grim details of what happened in the killing spree were pieced together from Somalis who escaped or who hid Harti, and from Western relief workers whose agencies have tried to protect Harti employees.

Many Somalis interviewed in the last two days said they wanted the story to get out but, fearful of retribution, they insisted on anonymity.

One survivor, a man in his 20’s, said he was blindfolded with five others after loyalists to Colonel Jess broke into his house at 3 A.M. on Dec. 9. He said the women in the house were beaten with guns and the men were driven in a “technical” — a souped-up jeep with weapons mounted on it — to the beach.

The four Harti in the group were lined up and shot without questions, the survivor said in an interview here. The survivor and another man pleaded with the gunmen that they were not Hartis, and the killers took them to a Jess encampment until morning, then released them. A Surgeon Is Shot

One of the five Somali doctors at the Kismayu hospital, Mohammed Musa Sugule, a Harti, was shot in front of his wife and children, according to several Somalis and to an account given to Reginald Moreels, the president of the medical agency Doctors Without Borders.

Dr. Moreels, who arrived in Kismayu on Dec. 12, said he was told by a doctor at the hospital that Dr. Sugule, a well-known surgeon, left work one evening and joined his family in a place where there was “quarreling” with Jess fighters. Dr. Sugule was shot in the head, Dr. Moreels said.

“In the whole week after my arrival, there was a lot of clannic cleaning,” Dr. Moreels said in an interview from Brussels. “I was struck by the hate among the people. A lot of people were shot to be killed — they were shot in the head, the thorax, the abdomen. In war there are two types of injuries: to the limbs to handicap or, as in this case, to kill.” A Confusion of U.S. Goals

The American-led military intervention in Somalia has been repeatedly described by Washington as limited to securing routes for the delivery of aid.

But in the nearly three weeks since the troops landed, it has become clear that because so many of the hungry died before the foreign forces arrived, emergency food is perhaps a less critical issue than was originally outlined. Just as important now, say Western diplomats, aid workers and Somalis, is the need for political reconciliation, to allow Somalia some semblance of normality.

In the late afternoon before the Americans landed on the beach of Mogadishu, Colonel Jess called a rally in Kismayu and said the town had to be “cleared” of people who would cause problems, a member of his central committee said in an interview. The committee is a 74-member Ogadeni group, the Somali Patrotic Movement.

This was the go-ahead for the killings, the committee member said, adding that it was “obvious” that Colonel Jess’s main ally, General Aidid, was in collusion. General Aidid visited Kismayu briefly on Dec. 6, two days before the start of the killings. A Warning From the U.S.

Mr. Oakley, the Presidential envoy, said in an interview Saturday that he believed “over 100” people were killed in the clan purge. Mr. Oakley said he had told the Colonel that “we knew exactly what went on and we won’t forget it.”

The envoy, who visited each Somali town ahead of the troops to explain their role to local leaders, suggested that Washington’s possible response to the killings was limited. He said the Security Council resolution authorizing military intervention in Somalia made no provisions for trying suspects charged with war crimes.

“The legal situation is very clear,” Mr. Oakley said. “We are not an occupying power. We have no power of arrest. There is nothing in the Security Council resolution about war crimes, as there is with Bosnia.”

A Western diplomat acknowledged that by dealing with local leaders like Colonel Jess, the foreign forces ran the risk of giving them legitimacy. “Kismayu is a political problem, not a humanitarian problem,” the diplomat said. An Attempt at Isolation

Instead of taking direct action against Colonel Jess, Mr. Oakley said, attempts would be made to isolate him by encouraging traditional leaders to take part in new town committees. The American troops, joined by Belgians here, made their first moves against Colonel Jess today by surrounding a compound where he keeps a number of armed vehicles, with the apparent intention of confiscating them.

Kismayu, which has a reputation in Somalia as a particularly vicious and volatile town, has been battered by waves of occupying armies over the past two years of Somalia’s civil war. But the killings in early December were the most systematic and brutal, Somalis witnesses said.

Dr. Moreels, of Doctors Without Borders, who stayed in Kismayu until Dec. 22, said he worked on “hundreds of war wounded” in the time he was there.

On his arrival, Dr. Moreels said, he went to see Colonel Jess to seek a guarantee that all the people, no matter what clan, would have access to the hospital. Many Harti, he said, were afraid to come to the hospital and Harti staff members were too scared to leave the hospital grounds, he said. ‘Just a Little Problem’

“Jess said it was just a little problem one night and things would go better,” Dr. Moreels said. “It was a complete lie because all the nights there were clannic cleanings.”

One of the most prominent people killed was Ali Warabe, a Harti elder, several Somalis said. His body, stripped of his expensive sarong, was found with nine others at Gobuen, 10 miles north of the city, according to a Somali friend. Among others in the group, all blindfolded, were Mohammed Abdi Hersi and Gura Hadji, two senior members of the clan.

Aid workers said they knew of one Harti man who had lost 17 members of his family in the purge.

For the Harti who escaped, daily life became a torment of fear.

A young educated Harti who supervises a center for an international aid agency in Kismayu said he was grabbed on Dec. 14 at the center and surrounded by five armed Ogadeni men who said they wanted to kill him.

“They shouted at me: ‘How can a Harti man work in a place occupied by the Somali National Alliance, especially in such a post,’ ” the young man recalled, a references to the group formed by Colonel Jess and General Aidid.

He was saved, the young man said, by sympathetic workers at the center who outmaneuvered the attackers. A Smooth Character

The killings in Kismayu did not seem out of character for Colonel Jess, both Americans and Somalis said. He is described as showing a smooth veneer and being practiced at a vocabulary that he thinks will impress Westerners; his public speech to Mr. Oakley on Dec. 19 was full of references to the emerging democracy in Somalia.

But, above all, he is known as a ruthless military man.

He was also a close colleague of Gen. Mohammed Said Hersi Morgan, the son-in-law of the ousted President, Mohammed Siad Barre, when General Morgan masterminded a war in 1988 against the Isaak clan in the northeastern city of Hargeisa.

Colonel Jess attended medical school in Italy, the former colonial power of the southern part of Somalia, but never finished, a colleague said. He received his military training in the former Soviet Union.

A member of Colonel Jess’s alliance said that three days after the killings began, a senior member of the central committee, Ali Haidar Ismael, criticized the colonel in public and called him a “criminal.”

The committee member said the colonel replied that he was not a criminal, and that the actions were the recommendation of the alliance’s “security committee” as “necessary for the security of the country.”

Allkisima News Desk

Diiwaanka Wararka

Xafiiska/Nashville-Tennessee-USA.