"The contents of the documents give solid grounds to doubt that the president of Russia took a direct part in finalising the text of the order," said a statement by the policy-making Security Council.
Yeltsin has ordered Alexander Lebed, the secretary of the Security Council and his personal representative in Chechnya, to restore Russian control over the regional capital Grozny, much of which was seized by separatist rebels on August 6.
Yeltsin's press secretary Sergei Yastrzhembsky said on Monday that the Kremlin leader had issued the order on Sunday.
But the Security Council's statement argued that Lebed was not aware of the preparation of the orders -- which violated normal procedures.
The statement also said Yeltsin's orders were issued with a facsimile of the president's signature rather than signed by the president in person.
"The secretary of the Security Council assumes that no one is allowed to manipulate on behalf of the President and insists on explanations from the appropriate officials," it said.
It said an attempt to carry out the order on Chechnya would ruin peace efforts undertaken by Lebed and wreck a ceasefire deal he agreed with the separatist leaders.
"This would mean in fact the beginning of a large-scale military operation involving aviation and artillery, which would naturally lead to heavy losses among federal troops, massive deaths among the civilian population...and a justified burst of resentment in the country," the statement said.
Lebed and rebel leaders agreed last week to arrange a truce to allow peace negotiations to resume in a region wracked by conflict which has cost tens of thousands of lives in 20 months.
The truce had been generally observed by both sides despite the lack of a clear deal between the sides and mutual recriminations over ceasefire violations.
On Monday Russia's top commander in Chechnya, Konstantin Pulikovsky, gave the rebels 48 hours to leave Grozny or face bombing.
Yeltsin, 65, has disappeared from the public eye since late June, except for a brief appearance at his inauguration on August 9, but his aides say his health is all right despite exhaustion caused by his vigorous re-election campaign.
Yastrzhembsky said on Tuesday that Yeltsin had begun a two-day break in northwestern Russia, denying rumours that the Kremlin leader was ill.
He said Yeltsin and Prime Minister Viktor Chernomyrdin were continuing to work on the formation of the new Russian government, most of which was announced last week.
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