Conflict between the civilian and military branches of Mr Suharto's government raises the stakes in a crisis that claimed 500 lives in rioting last week.
After a day of extraordinary scenes in the national parliament, where thousands of student demonstrators chanted slogans calling for the President to be hanged, the Speaker, Harmoko, asked Mr Suharto to resign, amid violent unrest against his 32-year rule.
"The Speaker of the House, along with his deputies, hopes for unity amongst the nation and that the President will wisely step down," said Mr Harmoko, a former minister and crony of Mr Suharto's who ranks third in the hierarchy after the President and Vice-President.
The call for his resignation from a parliament which for 30 years has never once challenged the President appeared to deal a mortal blow to Mr Suharto, who has become a figure of universal loathing among ordinary Indonesians. But last night, after four hours of speculation, General Wiranto, commander-in-chief of the armed forces, announced that the statement was illegal.
"The Indonesian armed forces (Abri) understand this to be an individual opinion with no legal power," he told a press conference.
"Abri thinks it is the duty of the President to administer the government and to reshuffle the Cabinet, to implement total reform and handle the crisis. This is crucial and with it Indonesia can move out of the period of crisis."
The country wakes this morning to the prospect of a president with no supporters other than his senior officers, and even their loyalty is uncertain.
Rumours persist of a power struggle between General Wiranto and the commander of the elite Strategic Reserve, Lieutenant-General Prabowo Subianto, who is also a son-in-law of Mr Suharto.
The President's intelligence chief said that Mr Suharto would respond to Mr Harmoko today, on the eve of what promise to be the biggest and potentially the most violent demonstrations yet.
Millions of protesters are expected to turn out in the cities around Indonesia tomorrow on the 90th anniversary of the foundation of the Indonesian nationalist movement.
"It is easy for the nation to be destroyed," General Wiranto warned the protesters last night. "So I call on those people who want to provoke anarchy to think again and desist from their activities."
But Amien Rais, a Muslim intellectual who has led the campaign for Mr Suharto's resignation, insisted that the demonstrations would still go ahead.
"Labourers, fishermen, housewives and students now have one single demand - that Suharto must step down," Mr Rais told a committee in the parliament building. "Anything else is cosmetic; a Cabinet reshuffle is just a political cosmetic and it is not going to help."
Mr Suharto promised over the weekend to reshuffle his Cabinet, which includes close friends and his eldest daughter. But yesterday only the minister for tourism had handed in his notice. General Wiranto blamed last week's riots - in which, in addition to the loss of life, 3,000 buildings were destroyed in Jakarta alone - on Indonesians who "were tempted, provoked and supported by irresponsible people motivated by their own or others' interests".
He recommended setting up a "reform committee" including officials and civilians.
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