The lower house of parliament voted by 277 votes to seven with four abstentions for a resolution calling for the head of Vladimir Kvasov, who was in charge of admissions to Friday's sessions.
Deputies said that they were turned back at the Spassky Gate in Red Square as they arrived for the session in the Marble Hall of the Kremlin.
Others deputies had been allowed through earlier.
Communist deputy Vladimir Semago called the occurrence a "humiliating way of treating" the Duma.
Kvasov brushed off the vote as a piece of summertime madness from the Duma and said he would not resign.
"I've been sacked by someone or other five or six times," he told The Moscow Times. "This will be the seventh. I have not resigned. This tells us yet again about the intellectual level of the Duma."
Only Prime Minister Viktor Chernomyrdin, a close associate of Kvasov, has the power to dismiss him.
Kvasov said that 42 places had been set aside for Duma deputies and that those who were turned away were not on the agreed list of parliamentarians. He said others who waited were allowed in later even though they were not on the list.
But deputies in the Duma said several had been turned away who were on the list.
Deputies who were let into the session were surprised when told about the vote in the Duma.
Vladimir Zhirinovsky, the eccentric ultranationalist who might have been expected to lead an attack on the government inside the Duma, said indulgently that "there weren't enough places" but expressed no outrage at his colleagues' treatment. Zhirinovsky said the session should have been held in the larger Palace of Congresses.
Sergei Shakhrai, leader of the centrist PRES faction in the Duma, blamed "organizational confusion" on the mistake but also played down the dispute.
Even before Friday's row Kvasov was a figure with many enemies in the parliament and the president's administration.
As head of the government apparatus, Kvasov wields immense power and is effectively the top bureaucrat in the country. President Boris Yeltsin publicly reprimanded him last month forhis handling of the apparatus and reformists have blamed him for slowing down the implementation of economic reform.
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