Rumours about the existence of such a faction have circulated in the US capital for a long time, but the comments by Peter Hoekstra, chairman of the House Intelligence Committee, mark the first time they were corroborated by an official with knowledge of the intelligence community.
"In fact, I have been long concerned that a strong and well-positioned group within the agency intentionally undermined the administration and its policies," Hoekstra wrote in a letter to Bush dated May 18.
The CIA declined to comment.
The document was obtained by The New York Times and posted on its website. Hoekstra confirmed its authenticity in a television interview on Sunday, but did not elaborate on his concerns.
The allegations stem from a CIA leak investigation centred on Valerie Plame, a former agency operative whose husband, retired ambassador Joseph Wilson, made a trip to Niger in 2002 to check on reports that Iraq had secretly tried to buy uranium ore there.
The Bush administration had used those reports to accuse the government of Saddam Hussein of trying to build a nuclear arsenal, claims that were used to justify the US-led invasion of the country in March 2003.
Plame's name was disclosed to the public in July 2003 by conservative columnist Robert Novak after her husband accused the Bush administration in a newspaper article of "exaggerating the Iraqi threat".
Lewis Libby (L) was indicted in
connection with the Plame leak
Lewis "Scooter" Libby, a former chief of staff for Dick Cheney, the vice-president, was indicted in connection with revealing the cover of the secret agent.
Libby was the first to hint publicly at the existence of a dissident faction inside the CIA in a New York Times interview before his indictment in October.
He was quoted as saying the CIA was engaged in a "perverted war" over the war in Iraq and resorted to "selective leaking" of information to drive its point home.
He insisted that Wilson had been sent to Niger by people within the CIA without the knowledge of George Tenet, who was then director of central intelligence, or the White House.
Not for publication
Hoekstra, whose letter was not intended for publication, said his argument about the faction was supported by the Plame affair "as well as by the string of unauthorised disclosures from an organisation that prides itself with being able to keep secrets".
The chairman went on to name some names.
They included Stephen Kappes, a former CIA director of operations who is slated to become deputy director of the agency.
Hoekstra expressed concern that Kappes, who quit the agency in 2004 after Porter Goss became its director, "may have been part of this group", noting that it was suspicious that Democrats on his committees "now publicly support Mr Kappes's return".
A close associate of Kappes’s, Michael Sulick, was named in the letter as another dissident suspect.
"Every day we suffer from the consequences of individuals promoting their personal agendas," Hoekstra wrote, referring to the situation at the CIA. "This is clearly a place at which we do not want or need to be."
Hoekstra publicly opposed the appointment of the current agency director, General Michael Hayden, calling him "the wrong man at the wrong place at the wrong time".