Lindsay Murdoch, Darwin – Deposed prime minister Mari Alkatiri has accused the Catholic Church's hierarchy in East Timor of being behind a conspiracy to destroy his Fretilin Government.

Mr Alkatiri lashed out at the church's leaders in an interview before leaving East Timor for Portugal for medical treatment on Wednesday, saying the main reason they wanted to depose him was because he is not Catholic. "I don't say it was the whole of the Catholic Church. But it was the hierarchy," Mr Alkatiri said. "And they were joined by other groups... people from the opposition parties and illegal groups within the country."

Mr Alkatiri is a Muslim in a country in which 96 per cent of its 1 million people are Catholics and the Catholic Church is by far the most powerful institution.

Since being forced from office amid violence in June, he has refused to say who he believes was behind what he says was a well-planned conspiracy to topple him. But he told the online Southeast Asian Times the plot started in 2001 and included three weeks of street protests last year during which he refused repeated calls to stand down.

"Since then they were always trying to get support from institutions and individuals within the country... always with the same purpose: to force the Government to step down." He said a "sense of impunity" surrounded army mutineers and prison escapees and called on Australian troops to arrest them.

President Xanana Gusmao and Prime Minister Jose Ramos Horta lacked the courage to defend the constitution when violence flared in Dili in April and May, he said. Mr Alkatiri is being investigated for alleged links with a civilian hit squad set up to kill political opponents, which he denies.

Domingos Soares, Catholic Church spokesman in Dili, said the church would not respond to his claims.