Sir Jock said the Afghan army would not be able to take over security until 2014 - a year later than the current US estimate, which he said was "a little optimistic".
Challenged about a front page story in The Independent on Sunday questioning the mission, he said: "It is true that al-Qaeda are not operating in Afghanistan at the moment. It is also true that over the last couple of years in particular the al-Qaeda core has suffered significant damage".
That did not mean "that they could not come back, that they are finished for good" but if pressure on them continued "they could be," he argued.
He rejected the argument of former foreign office minister Kim Howells that Britain would be better off pulling out its troops and switching resources to building up security at home.
"You can't defend just on the goal-line. That won't work," he said.
'Clear military progress'
Air Chief Marshal Stirrup's comments came as hundreds of people gathered in London for the annual Remembrance service and British troops at Camp Bastion, in Afghanistan, remembered the fallen on a day another soldier was killed, taking the British death toll to 231.
Turning to strategy on the ground, Sir Jock confirmed the international force (ISAF) would focus more on the main population centres in Afghanistan - but he denied Britain was planning to pull out of the key Helmand town of Musa Qala, which was retaken from the Taleban amid heavy fighting in 2007.
This campaign is directly connected to our safety back here in the United Kingdom and people need to recognise that
Bob Ainsworth, defence secretary
He also acknowledged there was frustration in London at Washington's delay in sending more troops to Afghanistan, saying the current strategy requires more force "and if that force is not forthcoming we will have to think again".
Prime Minister Gordon Brown told the Politics Show that the government had a "duty" to set set out the reasons behind the Afghanistan operation whenever questions are raised.
"It's right that we explain there is a chain of terror that links Pakistan and the Afghanistan-Pakistan border to the streets of our cities in Britain," Mr Brown said.
But giving his reaction to the poll, Scotland's first minister Alex Salmond said withdrawal of troops must now be considered.
"There has to be the fundamental reassessment of the role, mission, strategy - nothing should be off the table, that should include the possibility of a withdrawal."
In a poll for the BBC's Politics Show, 42% of the 1,009 adults surveyed said they did not understand the purpose of Britain's mission in Afghanistan.
Some 63% of those surveyed felt UK troops should be withdrawn as soon as possible, and 52% agreed that levels of corruption in Afghanistan's government meant the war was "not worth fighting for".
Defence Secretary Bob Ainsworth acknowledged public opinion had been "dented" by recent losses, but added: "We cannot run a campaign like this off the back of an opinion poll."
William Hague: "It is still possible to succeed"
He told Sky News: "We have to persevere, we have to show some resolution.
"This campaign is directly connected to our safety back here in the United Kingdom and people need to recognise that. Failure will be a disaster for us."
The government's strategy on Afghanistan has come under heavy scrutiny in a week in which five British soldiers were killed in an attack by an Afghan police officer.
So far, 94 UK service personnel have been killed in 2009 - the highest toll in a single year since the Falklands campaign 27 years ago.
Shadow foreign secretary William Hague backed calls for a better communications strategy, but said "actual military success" also had to be demonstrated.
He said: "Public support would not be sustained for a campaign of that length in which we could not show really clear military and political progress in Afghanistan."
The senior UK commander in Afghanistan, Lt Gen Jim Dutton, echoed these comments, saying in an interview with BBC One's Politics Show that the public "have to believe that we can win".
The number of British military personnel killed on operations in Afghanistan since 2001 stands at 232.
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