The ambitious reserve general, whose political career could depend on success in Chechnya, said he would meet the president on Friday to discuss a peace plan negotiated in Chechnya on Thursday.
But Yeltsin's office said no meeting was planned.
Hours before Lebed struck the deal in Chechnya, Yeltsin criticised him for acting too slowly to end the 20-month war.
He has since made no comment on the truce, which began at noon (0800GMT).
Grozny was relatively calm on Friday and both Russian soldiers and Chechen fighters said the ceasefire was holding.
Preparations are going on now for the withdrawal of units from southern districts of the republic to the Chechen plain, Interfax quoted the Russian command in Chechnya as saying.
Lebed, a reserve paratroop general appointed by Yeltsin last week to settle the conflict, said he had been given full command of operations there and would meet Yeltsin in the afternoon.
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I'm in command here. I have legitimate authority to fulfil the duties I have been charged with, Interfax news agency quoted him as saying on his return to Moscow early on Friday.
But Lebed's powers have never been clearly defined in public and the chain of command has been tangled in recent days.
It will take tough words from Yeltsin to convince Russia's military hawks, humiliated by the rebels' seizure of the Chechen capital Grozny this month, they should give Lebed a chance.
The signs are not encouraging so far.
The head of Russia's North Caucasus military district, which includes Chechnya, noted ceasefires have come and gone before.
Yeltsin said of Lebed on Thursday: He always promised to solve the Chechnya problem if he had power. Now he has power.
But unfortunately the results of his work are not yet obvious. But we will not despair. We will take the issue to the end, he added. Izvestia newspaper said the criticism raised serious questions and hinted that the president was out of touch.
Either the president is still demanding the impossible