Six years after Indonesia forcibly annexed the former Portuguese colony of East Timor, guerrillas seeking independence for the rugged territory are still holding out in mountain redoubts. But their strength appears to be waning as the Indonesians carry out a large-scale resettlement of rural inhabitants aimed at denying the guerrillas food and support.

The Indonesians have been pouring development funds into the impoverished, predominantly Roman Catholic territory after centuries of neglect under the Portuguese. But the resettlement campaign and restrictions on villagers' movements have alienated many already distrustful East Timorese, led to charges of human rights abuses and disrupted the farming that barely sustains the population in normal times.

One result has been the worsening of chronic food shortages in some areas of a land that is already suffering from severe drought. But while malnutrition is a problem, a famine anticipated by some Catholic church sources and Western journalists has not materialized.

These conclusions are based on interviews with relief officials, Western diplomats and Indonesian sources who recently visited East Timor, 400 miles off the northern coast of Australia.

The interviews indicated that the main source of concern about East Timor now is the continued detention of thousands of relatives and supporters of the Revolutionary Front for an Independent East Timor, known by its Portuguese abbreviation Fretilin.

After a year of turmoil following the 1974 Portuguese revolution and introduction of a decolonization policy, Fretilin won a three-month civil war and declared the Democratic Republic of East Timor on Nov. 28, 1975.

Fearing the emergence of a leftist government on the eastern half of the island--the Western side has long been undisputed Indonesian territory--Jakarta abandoned covert efforts to build up its allies in East Timor and launched an invasion to take it over.

The warfare between the Indonesians and Fretilin forces further disrupted the fragile agrarian economy and caused heavy casualties. By 1979, foreign relief workers and Indonesian officials estimated that about 100,000 East Timorese, nearly one-sixth of the estimated pre-1975 population, had died since the civil war. Most were victims of famine and disease caused by the war's disruptions and the government's subsequent neglect.

Since then, the Indonesian government, encouraged by the United States, has made a major effort to develop East Timor, building new roads, schools and hospitals and shipping in tons of food.

At the same time, military operations against Fretilin remnants have continued. According to well-informed diplomats, the guerrillas now are estimated to number no more than 300, with insufficient weapons.

Nevertheless, Fretilin still engages Indonesian forces in one or two small clashes a month, with occasional upsurges of rebel activity, according to diplomats and Indonesian sources.

While many East Timorese may be hostile to the Indonesian government, the area by and large has been pacified, and Jakarta has allowed about 60 foreign visitors to travel there in the past year.

However, apparently stung by foreign criticism -- and despite a professed policy of increasing access to the restricted, military-controlled region--Indonesian authorities refused to allow me to visit East Timor to look into reports of continuing food shortages and human rights violations. Nor would any Indonesian military official agree to be interviewed about East Timor.

Some of the current Indonesian sensitivity evidently stems from a U.N. resolution calling for self-determination in East Timor. Indonesia says self-determination has already taken place, with a 1978 vote by local councils to "incorporate" with Indonesia as its 27th province.

The U.N. resolution has passed by steadily dwindling margins in recent years, and Indonesia hopes eventually to remove it from the. General Assembly's agenda.

On the human rights questions, U.S. officials have said they are pursuing a policy of "quiet diplomacy" with the Indonesian government, but some Indonesian officials suggest the Reagan administration approach might be more akin to "silent diplomacy."

Asked by reporters whether the issue was raised during the visit to Washington last month of Indonesian President Suharto, Assistant Secretary of State for East Asian and Pacific Affairs John Holdridge, who has been nominated to become the next ambassador to Jakarta, said only that all subjects of importance were covered.

However, Foreign Minister Mochtar Kusumaatmadja said in an interview here that East Timor had not come up in talks with President Reagan or other administration officials during the visit. He said U.S. concerns had been conveyed months before, with the American Embassy expressing interest in increased access to the territory for its officials and other visitors.

In testimony in September before the House subcommittee on Asian and Pacific affairs, Holdridge spoke of a general improvement in the human rights situation in East Timor. His report contrasted sharply with testimony before the same subcommittee by Michael Williams, the head of Amnesty International's Asia research department.

Williams cited an Indonesian "occupation of extraordinary brutality in which a whole range of fundamental human rights have been denied the population, adding: "Amnesty International believes that the population of East Timor has been systematically denied the rights to freedom of expression, association, assembly and movement."

Williams also said there have been arbitrary detentions, forced conscriptions and other severe restrictions on people's daily lives. He added that "Amnesty International has received frequent reports of random violence by Indonesian soldiers on the streets and in private houses and of sexual abuse."

The London-based human rights organization said its findings for the period 1977-81 "reveal recurrent waves of arrests, summary executions and 'disappearances' in these years."

Asked about the charges, Foreign Minister Mochtar said, "I think these are unfounded." He and other officials in Jakarta referred questions about specific allegations to the International Committee of the Red Cross, which does not disclose details of its findings to any party except the government concerned.

An unofficial adviser to President Suharto said of the allegations that prisoners have been tortured: "I don't think so. Not now. Maybe before."

While most of the abuses may indeed be a thing of the past, Indonesian authorities clearly are pressing ahead with controversial efforts to "relocate" East Timorese who are related to or support Fretilin guerrillas.

A much-criticized feature of these efforts is the continuing detention of nearly 4,000 people -- officially termed "temporarily displaced persons" -- on the tiny island of Atauro, 18 miles north of East Timor's capital, Dili.

The detainees have been moved from their homes in the interior to deny the Fretilin remnants a source of support. Amnesty International regards them as "political prisoners detained against their will," and has concluded that most of them are "virtual hostages for relatives" who still refuse to surrender.

Mochtar denied that they were being held hostage, but said he did not know the reason for their continued detention.

"For a time it had something to do with the security operation, to get them out of the way," he said.

"To understand the situation there, they are very, I would say, primitive," the foreign minister added. "There is still this vendetta mentality. You might as well say they are kept apart from the other people for their own protection."

The Fretilin relatives and supporters who surrendered first faced the rigorous move to Atauro, then the conditions at a detention camp built for them.

More than 170 detainees have died at the camp since mid-1980, about 60 of them from a severe outbreak of gastroenteritis at the end of last year, according to the Indonesian Red Cross. The International Committee of the Red Cross began a supplementary feeding program in April to alleviate malnutrition at the camp and introduced measures to improve health and hygiene.

Despite reported Indonesian assurances to visiting dignitaries that the detainees would be gradually resettled and the camp closed by year's end, the population has actually increased since the international committee counted 3,280 persons at the camp in February.

When a diplomatic delegation visited Atauro at the end of September, there were 4,077 detainees in the camp. One of the visitors called it "a dreary place" built on barren land with a chronic shortage of water.

A major concern of foreign visitors to Atauro is that its subsistence agriculture cannot adequately feed more than the 5,200 permanent residents of the 4-by-12-mile island.

"The fact of bringing in 4,000 more people has completely unbalanced the island and could harm its ecology," one recent visitor said. He cited the detainees' need to cut trees for firewood as one damaging factor.

Still, the extent of malnutrition generally is considered no more serious on East Timor than it is on the western half and other poor islands in the archipelago. According to relief sources, most of the food shortages have nothing to do with the Indonesian annexation and its aftermath.

As for the future, Indonesian officials are confident that East Timorese and the rest of the world will eventually accept the "integration" of the territory into Indonesia.

"The Fretilin have ceased to exist practically," said Foreign Minister Mochtar. "If they don't give themselves up, it is because they fear reprisals. They no longer have any cause."