General Sir Richard Dannatt also said in an interview with the Daily Mail newspaper on Friday that Britain's Iraq venture was aggravating the security threat elsewhere in the world.
In unusually blunt comments for a serving senior officer, Dannatt told the Friday edition of the newspaper that the troops should "get ... out sometime soon because our presence exacerbates the security problems".
Britain, Washington's main ally in Iraq, has about 7,000 soldiers deployed, mainly in the south of the country.
The US-led invasion to oust Saddam Hussein, then the Iraqi president, has come under heavy criticism, as the civilian death toll mounts and British and US troops are increasingly in the firing line.
A spokesman for Tony Blair's office, speaking on condition of anonymity, said: "It's important that people remember that we are in Iraq at the express wish of the democratically elected Iraqi government."
The British prime minister's official spokesman said in Scotland that the general had Blair's full support.
Later in the day, however, Dannat said he meant a phased withdrawal over two or three years, and denied that he was attacking government policy.
The army chief insisted on Friday morning that Britain stood "shoulder to shoulder with the Americans, and their timing and our timing are one and the same".
"We'll probably reduce our soldiers over the course of the next year or two or three - let's wait and see. That's what I mean by sometime soon," Dannatt said in an interview with Sky News.
And he said in an interview with BBC radio: "We don't do surrender. We don't pull down white flags. We're going to see this through."
Daily Mail interview
In the controversial Daily Mail interview, Dannatt, who took over as chief of the general staff in August, said: "We are in a Muslim country and Muslims' views of foreigners in their country are quite clear. As a foreigner, you can be welcomed by being invited in a country, but we weren't invited certainly by those in Iraq at the time.
"The military campaign we fought in 2003 effectively kicked the door in. Whatever consent we may have had in the first place, may have turned to tolerance and has largely turned to intolerance.
"That is a fact. I don't say that the difficulties we are experiencing round the world are caused by our presence in Iraq, but undoubtedly our presence in Iraq exacerbates them."
Putting himself directly at odds with Blair and George Bush, the US president, the general criticised the post-invasion planning by the US-led forces.
"I think history will show that the planning for what happened after the initial successful war fighting phase was poor, probably based more on optimism than sound planning.
"I think history will show that the planning for what happened after the initial successful war fighting phase was poor, probably based more on optimism than sound planning"
General Sir Richard Dannatt, chief of Britain's army
"The original intention was that we put in place a liberal democracy that was an exemplar for the region, was pro-West and might have a beneficial effect on the balance within the Middle East. That was the hope, whether that was a sensible or naive hope history will judge. I don't think we are going to do that. I think we should aim for a lower ambition."
Foreign troops needed
The Iraqi government has responded by saying it still needs British and US forces to help stabilise the country.
Ali al-Dabbagh, a government spokesman, said on Friday he expected that British troops would be staying for the near future.
The British government has "confirmed its support to the Iraqi government", he said. "The presence of these forces is necessary so that they can participate in establishing stability in Iraq.
"The Iraqi government does not wish to keep the foreign forces forever but these forces are staying for the time being, under a request by the Iraqi government and according to the international resolutions," he added.