"I have consistently said since I arrived here that there is no place in the new Iraq" for militias, he told the coalition run television channel Al-Iraqiya on Friday night.
"Our definition of a militia is an organisation which is not national," he said, according to the channel's simultaneous Arabic translation.
"The national organisations we have promised to construct are the new Iraqi army and the new Iraqi police force and the civil defence force. These are national organisations.
"We have welcomed the militias' cooperation with the national authorities, but they cannot continue as militias.
"Quite simply the presence of militias does not fit into the campaign of building an independent Iraq with an army and police," Bremer said in an interview for a TV programme.
Interim foreign minister Hoshyar Zebari backed the use of militiamen as Iraq wrestles with armed resistance to the US-led occupation.
Zebari hailed the idea of recruiting former members of militias, including those of his own Kurdistan Democratic Party, for a new counter-insurgency battalion to work with US Special Forces.
The Kurds' Peshmerga militias
helped the US oust Saddam
"I think this is a wise move," he told CNN. "It has come too late, but it is better late than never," he added, referring to the coalition's rejection of the idea when it was first put forward by former exiled groups in late May.
The minister said that he thought a "political force" of reliable anti-Saddam fighters could help play a vital role in stemming the violence hitting coalition soldiers, Iraqi civilians and economic infrastructure.