Senate buildings have been closed for two months
The denial came after the Washington Post quoted scientists investigating anthrax mailed to Capitol Hill as saying that tests had found it identical to a strain developed by US Army scientists at Fort Detrick in Maryland.
Both the US Army and the Central Intelligence Agency say the bacteria was in a different, powdered form from their stocks, and could not have come from their programmes.
FBI sources have said a possible CIA link is being investigated because of a contractor who used to work in the agency's anthrax project.
Liquid strain
Fort Detrick is home to the US Army Medical Research Institute of Infectious Disease.
A spokesman, Chuck Dasey, said the research institute's supply had come from the Agriculture Department.
It had then been shared with up to five other labs - three of them in the US, one in Canada and one at Porton Down in the UK.
Mr Dasey was dismissive of the scientists' reported discovery. "I'm not sure it tells us anything about who the perpetrator is," he told the Associated Press.
"You can't say it all came from USAMRIID."
Scientists at Fort Detrick use the liquid strain of anthrax in research, Mr Dasey said.
"The point is we don't have the technology to make that fine dry powder which was in the letters."
The CIA was even more sure.
A spokesman, Mark Mansfield, said the anthrax sent in letters to Senators Tom Daschle and Patrick Leahy "absolutely did not come from CIA labs".
Five dead
The tainted letters were sent to the senators on 9 October from an address in Trenton, New Jersey, and sparked widespread fear following the suicide airliner attacks the previous month.
Anthrax letters were also sent to three media organisations.
Five people have died and 13 have been infected with the disease.
The investigation has recently been downplaying early suggestions that the anthrax bacteria came from another country's biological weapons programme.
Instead the FBI has in recent weeks been turning its attention towards a domestic source.