DILI, Indonesia, Oct 13, Reuter - Independence protests during Pope John Paul's mass in East Timor will have no effect on Indonesian plans to pull troops out of the disputed territory, a well-placed military source said on Friday.

"Jakarta has decided it is time to scale down. It's not the kind of decision you reverse because of a few kids with banners," said the source, who is closely involved in the troop presence in the territory but who asked not to be identified.

Witnesses said up to 100 protesters on Thursday battled with police as the Pope told Indonesia to uphold human rights after years of death and destruction in East Timor where Jakarta's rule is still not recognised by the United Nations.

Vatican spokesman Joaquin Navarro-Valls said the Pope, on a five-day visit to Indonesia, had not been disturbed by the protests.

"He did not give it weight," said Navarro, who put the number of demonstrators at only about 20.

The protesters, mostly students, unfurled banners asking for the Pope's help in ending military oppression and giving support to the pro-independence Fretilin guerrilla movement.

Fretilin, which has only a few hundred guerrillas fighting in the hills, has been a thorn in Jakarta's side since Indonesian troops annexed the former Portuguese colony in 1975.

Indonesia's armed forces moved in after the Portuguese hastily left during a conflict in which the Fretilin party seemed to be defeating pro-Jakarta parties.

In Lisbon, Fretilin issued a statement saying it was disappointed with the Pope's visit which had endorsed Indonesian efforts to obtain international legitimacy for its control.

Amnesty International and other groups have accused Indonesian of repeatedly abusing human rights. An estimated 200,000 East Timorese have died since Indonesian troops swept into the largely Catholic territory.

"It's true the Indonesian army is not that clean. But Fretilin has done its mass killings too," said the military source.

He estimated half the population of East Timor were passive supporters of Fretilin and other anti-Indonesian groups.

Jakarta keeps some 20,000 troops in Timor, around a quarter of them combat forces, he said.

"My opinion is that we have more troops than we need in East Timor," provincial governor Mario Viegas Carrascalao told a news before the Pope's four-hour visit to Dili.

Government sources said Jakarta, which has controlled its forces in East Timor directly for nearly 14 years, plans to return them to regular district command in mid-October and will start pulling some troops out.

Political analysts say making troops answerable to regional commanders should help reduce human rights violations.

The Pope's call for more respect for humanity in East Timor was clearly addressed to the military, the analysts said. "He said as much as he possibly could," one commented.

"Respect for the lives which render life more human must be firmly assured," the Pope said at Thursday's mass.

An analyst said the reduction of Indonesia's troop strength may mark a turning point for East Timor, adding that military heavy-handedness was the greatest cause of resentment among Timorese.

"If they can scale that down, it is a good start," he said.