About 100,000 Ugandan refugees, many famished, have poured into the impoverished southern Sudan to flee what they describe as religious and tribal killings by troops loyal to the new government in Kampala.

Most are from Uganda's northern stretches, the home area of deposed dictator Idi Amin. Some were linked to his reign of terror by their positions in the administration or Army. In general, they are despised as Amin's "Sudanese mercenaries" because their tribes span the border and many have family on both sides.

Running through the patchwork of motives for the murders the refugees describe is a common, tragic irony: The very people reviled for association with Amin's brutality are now complaining that they are on the suffering end of similar brutality.

This border village, about 150 miles south of the southern Sudanese capital of Juba, has been swollen to 5,000 residents - five times its normal size - by Ugandan refugees arriving filled with hate and fear.

Another 3,000 Ugandans have crossed the border over the little bridge here and then moved on to seek help in other Sudanese villages in the region. About 20,000 more have entered Sudan and registered as refugees at the area's two other main crossing points, Kaji-Kaji and Nimule, according to Sudanese border officials.

In all, about 100,000 Ugandan refugees have entered Sudan since the fall of Amin, with two-thirds just moving across the porous border without registering and seeking shelter with individual Sudanese families or camping in the bush, according to Brig. Joseph Lagu, president of the Autonomous southern Sudan.

One is Moses Bakai, 23, a trader who twice fled his village of Aringa near Amin's home village of Arua. Bakai said he first crossed into Sudan when Kampala fell last April. He returned, he said, in response to an appeal for calm and against recrimination broadcast by President Yusufu Lule after he took over in Kampala.

But with the arrival last week of "Lule's men" in his village, Bakai said, he saw his wife, aunt, 6-year-old sister and his children of 6 months and 2 years killed with knives inside his house. Eyes blazing with rage and tears, he said the village men scattered as soldiers pulled down men's and boy's trousers and slit the throats of those who were circumcised - as are Moslems - before bursting into the huts and killing anyone in them, including babies like his own.

Bakai said he was unable to say whether the soldiers were Ugandan or from the Tanzanian expeditionary force that drove Amin from power.

Religion plays a role in the killings directed at Moslems, but that is only part of the problem. Although Amin's Kakwa tribe is part of Uganda's Moslem minority, the Mahdi tribe fleeing in equal numbers from Kampala's soldiers is mainly Christian. The Tanzanian and Ugandan troops themselves are a mixture of Moslem and Christian.

Whatever the web of reasons for the killing, Sudanese Army officers in charge of the border say they have heard too many stories like Bakai's to dismiss them.

In some cases they knew the victim. Movement was constant across this border between Arua, 46 miles south, and Yei, 46 miles north. Both were prosperous trading centers for smuggled goods from the nearby Zaire border. Canned French margarine and lollipops are on sale by the road.

One man they knew was Arua's police chief Capt. Adam Musa Ngila, who died because they say he remained loyally at his post waiting for the new government's troops to arrive. His daughter, Hawa Adam Musa, 25, a widow since the Entebbe fighting that preceded the fall of Kampala and the mother of four small children, fled to Sudan last week after Tanzanian soldiers took Ngila roughly from their house. Over the weekend, she said, her uncle arrived here with news that her father had his throat cut by soldiers in his office after they had asked him to show them where Amin was and he said he did not know.

Sudanese traders at Kaya accept Ugandan currency and in some cases, are giving away food to new refugees. The new arrivals are much worse off than those who fled ahead of the advancing Army with stocks of food, and grass to build their houses. These were often in cars and were channeled away from the border up to Yei. Now there is almost no fuel left.

Hundreds of abandoned cars and trucks stand at Kaya and Nimule. Well over 500 are at Yei, including buses, Land Rovers, government vehicles, sports cars and motorbikes. Only top former officials have been allowed to keep their cars and have the gasoline to use them. The others are waiting for the ownership to be verified.

At nimule, one room in the police post is filled with dusty office typewriters and copying machines expected to be returned to the Ugandan government. But it could be months before that happens - Nimule has a grass airstrip a three-mile walk from the town and no gasoline. No food has been flown in and the town has jumped from a population of 5,000 to 16,000 in six weeks.

Small dugout canoes have been rowed over the Nile from Uganda in dozens in the last few weeks. Many of these refugees are Christians with heavy crosses round the children's necks dangling on stomachs already swollen with malnutrition. A Nubian widow from Bombo with five children said none of them had eaten for two days.

In Yei, refugee commissioner Gale Manese pointed to women lying down: and said, "They say they are sick. They are not sick, just in pain from hunger. All day I hear nothing but complaints of the lack of food and I can do nothing. It is horrible. Wire to Juba for food every day - almost none has yet come."

Over the weekend, two groups of Amin's soldiers arrived 30 in one group with two Army ambulances and 31 in the second with their officers still with them. They were disarmed at the border and heaps of rockets, rifles, machine guns, bazookas and grenades lie here under Sudanese Army guard waiting for transport to Juba and eventually return to Uganda.

These soldiers were not all northerners or Moslems. One young Air Force officer was a Muganda from Kampala and would only say, "For six weeks I have been running from Entebbe."

Lagu said so far only Egypt has airlifted tents and medicine to the area. Corn sent from Kenya for flood relief is being diverted to the Ugandan refugees.

Asked if more help was expected from northern Sudan, in addition to some grain on the way down the Nile, Lagu said, "There is nothing to send in Khartoum. We must be helped by the international agencies."

The United Nations High Commissioner for Refugees representative, Kevin Lyonette, left Juba on Sunday saying an emergency appeal for $2 million worth of food and $500,000 for tarpaulins for shelter against the rainy season will be launched from Geneva this week. CAPTION: Picture, Ugandan former vice president Mustafa Adrisi, left, shown with Idi Amin in 1977 photo, is now living as a refugee in a comfortable house in the southern Sudan. UPI; Map, no caption, By Richard Furno - The Washington Post