The accusations, by Major-General Alexander Korzhakov in an interview with the weekly newspaper Argumenti i Fakti, bring into the open a struggle for political influence that the Russian media has cited as an important factor behind Mr Yeltsin's decisionto send troops into Chechnya.
General Korzhakov gave no names but seemed to target the prominent banker and businessman Vladimir Gusinsky, head of a conglomerate called Most Group. His offices in the Moscow Mayor's office were raided by armed masked men from General Korzhakov's security service on 2 December.
Most Group condemned "lying assertions of an openly insulting character", saying it would start a civil suit. It also called on the acting prosecutor general, Alexei Ilyushenko, to start criminal action in response to "threats to physically exterminate the leadership of Most Group".
A former KGB body guard often described in the media as a new Rasputin, General Korzhakov has been at Mr Yeltsin's side since 1985, standing with him on a tank in front of the Moscow White House during the 1991 putsch and organising the storming of the building in October 1993.
In the interview published yesterday he denied any political ambitions or any decisive role in policy towards Chechnya: "I say immediately - I have never engaged in politics myself and do not consider myself a career politician." But he then outlined a bizarre conspiracy theory rife with political implications and attacked "shaky liberals" who "have shown their lack of understanding of the need for decisive action in critical situations.
"The threat to society comes not from the security service but from those who tactlessly and impudently walk in downtown Moscow, guns in hand, under the very nose of the Moscow Mayor's Office, from the financial mafia "fostering a new generation of politicians" and trying to get a pocket government, from those who bribe state officials and pursue their own interests to the detriment of the interests of the Fatherland. We won't stop combating them."
Speculation that General Korzhakov had become one of Russia's most powerful figures began in earnest last month, fuelled by a letter he wrote to the Prime Minister, Viktor Chernomyrdin, telling him to drop plans to reform Russia's quota system for oil exports. General Korzhakov yesterday defended the move - totally unrelated to security - as "quite normal".
Complaints in the media of undue influence, he suggested, were part of an "orchestrated campaign" of vilification engineered by his enemies. "It has been launched by the people we know as the `goose' flock and high-ranking officials closely linked to them. Let me note that I have long had a liking for goose hunting."
The name `Gusinsky' derives from the Russian word for goose and the comment seemed a thinly disguised attack on Mr Gusinsky, named last year as Russia's richest man and widely seen as a powerful political player because of his extensive media, banking and other business interests. As well as running Most Group, Mr Gusinsky has close ties with Moscow's Mayor, Yuri Luzhkov, and the liberal leader, Grigory Yavlinsky. Both supported Mr Yeltsin but are now seen as rivals because of their own presidential ambitions ahead of the 1996 election.
One theory for Mr Yeltsin's military venture in Chechnya is that he had hoped for a quick victory to boost his flagging political fortunes and neutralise potential rivals before the election.
Mr Gusinsky also controls the independent television channel NTV and the newspaper Segodnya, both of which have enraged Kremlin hardliners with their war reporting.