Indonesia admitted on Wednesday that soldiers had been entering mosques of a minority Islamic sect but said they had been protecting followers, escalating a debate about religious freedoms.

An Indonesian human rights group said however it had recorded 56 cases in West Java province in which soldiers forced Ahmadiyah followers to convert to mainstream Islam.

The government denies there have been any forced conversions, saying the military intervention was to protect the Ahmadiyah from more violence.

"As long as their intention is positive -- that is to ensure Ahmadiyah followers do not become the target of violence -- then that's not a human rights violation," said Justice and Human Rights Minister Patrialis Akbar.

"It’s not a harmful intervention," Akbar told reporters.

But local rights group Imparsial disputed that, saying soldiers have entered mosques, gathered the sect followers and "forced them to repent and convert to Islam".

There has been an international outcry over the treatment of Ahmadis after an amateur video showed hundreds of Muslim fanatics armed with machetes, sticks and rocks attacking Ahmadiyah followers, leaving three dead.

There is also criticism over a decree from some provincial administrations in the world's most populous Muslim country that prohibited Ahmadis from displaying signs identifying their mosques and schools.

"We already checked and there's no negative element, there's no coercion whatsoever," Defence Minister Purnomo Yusgiantoro said.

Human Rights Watch has condemned violence against the sect and urged President Susilo Bambang Yudhoyono to sack his religious affairs minister for discrimination and to lift the ban on Ahmadiyah practising in public.

Ahmadiyah, who differ from orthodox Muslims because they do not believe Mohammed was the last prophet, have been subjected to regular abuse and persecution since their sect was slapped with restrictions at the urging of mainstream Muslims in 2008.

Yudhoyono has condemned last month's attack on the sect but defended a 2008 law banning the Ahmadiyah from spreading their faith, which is used by hardliners to justify attacks on the sect.

Indonesia's constitution guarantees freedom of religion but rights groups say violence against minorities including Christians and Ahmadis has been escalating since 2008.

There have been cases of Christians being beaten and churches attacked.