Indonesia has ramped up pressure on the Howard government not to grant asylum to 43 Papuan boat people, with a senior minister denying that human rights abuses are systemic in the troubled province.

The Papuans case is threatening to intensify into a diplomatic row with a series of Indonesian leaders, from the president down, insisting that Canberra should send the group back.

Defence Minister Juwono Sudarsono challenged claims by the group of pro-independence activists of repression by Indonesian security forces.

"These were not asylum seekers because of internal repression by our police or military," he told foreign journalists. "But we find it difficult to persuade the media – international versus local – because this is a very popular notion about repression by the cruel Javanese over the poor Papuans for the past 15 years."

Sudarsono, a civilian who has pushed reform within Indonesia's military, said the issue should not harm growing defence ties, including the imminent resumption of training between Australian and Indonesian special forces soldiers.

Sudarsono is the third senior Indonesian official to pressure Australia in recent days, echoing the views of Foreign Minister Hassan Wirayuda and President Susilo Bambang Yudhoyono. Yudhoyono has telephoned Prime Minister John Howard to promise the Papuans would not be harmed if returned.

The Papuans have been taken to an immigration detention camp on Christmas Island, an Australian territory just south of Java, while their claims are being assessed.

Sudarsono admitted there had been sporadic incidents of violence against separatists but denied it was policy driven.

"I grant there have been incidents of some brutality and torture and rape involving some of our troops," he said. "But there is a tendency to blanket or insinuate that all these incidents are systemic."

He said Mr Howard had been "persuaded" the group should be returned as soon as possible, he said. "But of course its very difficult, because once it's in the hands of the immigration officers in Australia, then Australian law must operate on the ground there," Sudarsono said.

"I don't think it will destruct relations between defence ministries." The Papuans arrived in Australia last month after a five-day voyage in an outrigger canoe.

Sudarsono said reports from human rights groups that Indonesian army and police numbers in Papua were being almost doubled with an additional 15,000 soldiers to help crack down on separatists were nonsense.

The cash-strapped military could not even pay for an additional headquarters unit, let alone a division-strong deployment in the sprawling province, which Jakarta won sovereignty over in 1969 following a UN referendum widely seen as rigged.

If he tried to divert money earmarked for critical new combat aircraft, ships and military housing, then Jakarta would be abusing the human rights of its own troops, who receive "inadequate pay for a very important job", Sudarsono said.

Instead of a draconian security crackdown, the way forward lay in stronger efforts by mainstream political parties to win the support of Papuan voters.

"Some people are already disillusioned with democracy and parliamentary politics, and even some have openly cried for a return of the military," Sudarsono said "So the ball is in the court of our friends in the political parties, to get organised, get real and get things done on the ground."

But in calling for a strengthening of democracy, Sudarsono also defended a de facto ban of foreign media visiting Papua, warning it would only harm efforts to build more "unity and cohesion" and give a platform to disgruntled separatists.

He said there were many Indonesians, including members of the country's powerful elite, who harboured deep suspicions that foreign nations including Australia, the US and the Netherlands wanted to break up Indonesia.

"Your role as a magnetic attraction to Papuans of all stripes of political as well as ethnic sense of identity will create this sense of danger among people from outside of Papua that foreigners are trying to instill this sense of division," he said. "There is a clash of notions of human rights which I think you must understand."