Lindsay Murdoch, Jakarta – Indonesia's military yesterday pledged its loyalty to President Wahid after he suspended General Wiranto in an extraordinary back-flip just hours after declaring that he could remain in the Cabinet.

Ending a tense stand-off that was threatening Indonesia's transition from military to democratic rule, Mr Wahid removed General Wiranto as Co-ordinating Minister for Political and Security Affairs.

Appearing shattered, General Wiranto later admitted for the first time responsibility for the bloodbath in East Timor last year because he was the armed forces commander at the time.

But he denied any direct involvement and called for people to await the outcome of the Attorney-General's investigation into the violence. Speaking at the presidential palace, General Wiranto said: "I'm responsible for human rights abuses in East Timor ... that needs to be clarified by the Attorney-General before they take it to court."

For months he has rejected accusations by Indonesian and United Nations investigators that he was responsible for the military-backed violence in East Timor, and at times even tried to deny that it had happened.

General Wiranto told reporters that he refused to resign as Mr Wahid had repeatedly requested during the President's recent overseas trip because "I wanted to help him get a full report before he made the decision". "If there are changes, it is his right," he said. "Don't make it as a big matter."

After avoiding confronting General Wiranto during a meeting at the palace late on Sunday and saying he could remain pending the investigation, Mr Wahid prepared papers formalising the sacking and telephoned him with the news.

As Indonesians woke to find Mr Wahid had acted, the armed forces commander, Admiral Widodo, moved to dispel rumours that soldiers loyal to their former commander would act to remove Mr Wahid, the country's first democratically elected president.

"I, together with the navy, army and air force chiefs of staff, believe that what has been decided by the President has of course gone through a process of comprehensive consideration ... the President's decision is intended for the national interest." Admiral Widodo added: "Therefore all levels in the TNI [armed forces] are loyal and will safeguard the decision to be implemented in a good manner."

In a move indicating that Mr Wahid has no intention of bringing General Wiranto back into the Cabinet, the President announced that the Minister for Home Affairs, Lieutenant-General Surjadi Soedirdja, would take over his ministerial responsibilities. General Soedirdja is a former governor of Jakarta and member of Mr Wahid's National Awakening Party.

Mr Wahid, a frail Muslim cleric who was elected in October, has already promised that he will pardon General Wiranto if he is found guilty by an Indonesian court.

Before leaving the presidential palace, General Wiranto took a swipe at one of the army's highest-profile reforming officers, Major-General Agus Wirahadikusuma, who on Sunday had urged Mr Wahid to sack General Wiranto. General Wiranto said he felt "sad and guilty" because it had been his job to guide officers under his command. "I feel I have failed because those officers which I had trained have taken that kind of attitude ... they criticised me in a public forum. According to the officers' ethic code that's unethical."