Former armed forces minister Doug Henderson used the example of Vietnam, warning Britain might be seen by Afghans and other Muslims as being involved in an "imperial war".
Shadow defence secretary Bernard Jenkin said his party supported the deployment, but believed the Marines should be brought home as soon as the job of hunting down and eliminating remaining al-Qaeda militants was complete.
UK troops involved:
For more on their mission: Click here But Prime Minister Tony Blair strongly defended the deployment of 1,700 Marines at Prime Minister's Questions, telling MPs it was essential "to get the job done fully".
Mr Blair insisted there was "no mismatch" between the roles of the existing British peacekeeping force and the combat troops, under questioning by Liberal Democrat leader Charles Kennedy.
The number of al-Qaeda fighters still on the ground in Afghanistan could be in the hundreds or thousands, Defence Secretary Geoff Hoon said.
But it was "extraordinarily difficult" to tell until allied troops were on the ground, he added.
There has been unease about the mission among Labour backbenchers, with one former minister warning of parallels with the Vietnam War.
Meanwhile, Mr Jenkin - who sparked the debate through a little-used Commons' standing order - asked how long the mission would last.
Mr Hoon said: "Our exit strategy is that we will leave when the task is completed."
Liberal Democrat foreign affairs spokesman Menzies Campbell said that "in the war against terrorism, the commitment is always open-ended."
'Tough enemy'
Defence experts have raised fears that troops sent to flush-out al-Qaeda and Taleban forces from their remote mountain strongholds could face strong resistance.
Lieutenant Colonel Tim Chicken, of 45 Commando, has said morale is good and the troops are in "confident" mood.
But the "enemy are characteristically tough and well-defended", he added.
Major Charles Heyman, editor of Jane's World Armies, has claimed as many as 10,000 fighters could still be active in Afghanistan and in tribal areas of Pakistan.
But Mr Hoon rejected the idea that such a vast number of forces were assembled.
Former Labour minister Peter Kilfoyle said on Tuesday Britain was putting its troops into a "very murky, messy picture".
He added: "Of course, the precedent for the situation we find ourselves in is Vietnam and of course Harold Wilson, under great American pressure, kept us out."
The first marines are expected to begin arriving at Bagram airbase near Kabul over the next couple of days, with operations likely to start in the middle of April.
Casualties
Mr Hoon said fresh troops could be sent to replace the marines once their expected three-month deployment was over.
The force's commanding officer, Brigadier Roger Lane of 3 Commando Brigade, admitted there could be casualties.
He said: "You cannot undertake these [operations] without a degree of risk being involved - and that can be from non-combat injuries to being engaged by the opposition."
The decision to bring the total number of British forces involved in the war in Afghanistan to about 6,400 (there are 4,700 non-combat troops involved in security operations) was taken following negotiations with the US after Operation Anaconda ended.