Gen McChrystal and Mr Brown also held discussions in August
Prime Minister Gordon Brown has held a meeting with the US commander of Nato forces in Afghanistan, at which they agreed a need for more "Afghanisation".
Downing Street said this included speeding up training of the Afghan army and police, amid a growing insurgency.
Mr Brown had a "good discussion" with Gen Stanley McChrystal, who had earlier made a speech in London on Afghanistan.
Earlier Downing Street said the PM was "open-minded" about whether more UK troops were needed in the country.
The meeting with Gen McChrystal followed discussions the pair had in August during a visit by Mr Brown to Afghanistan, at which he also said the UK would be "stepping up" the training of Afghan soldiers.
In his speech to the International Institute for Strategic Studies on Thursday, Gen McChrystal warned there was only limited time to turn around the situation.
"The situation is serious and I choose that word very, very carefully," he said.
"Neither success nor failure in our endeavour in support of the Afghan people and government can be taken for granted. My best assessment is that the situation is in some ways deteriorating," he said.
I don't think that if we align our goals and resources we will have a significant problem - the problem will be if we don't
He called for more troops, stressing that it was essential that the mission had the resources it needed to complete its task.
"I don't think that if we align our goals and resources we will have a significant problem. The problem will be if we don't," he said.
On Thursday evening Downing Street said Mr Brown and Gen McChrystal had gone on to discuss the general's assessment of the campaign, and there was "agreement that the mission was at a vital stage".
"They looked forward to further discussion of General McChrystal's recommendations amongst Nato allies in coming weeks," a spokesperson added.
Earlier No 10 had said any increase in UK troop numbers in Afghanistan depended on the right strategy being in place and the necessary equipment being available for personnel.
Gordon Brown talks to Nick Robinson
Defence Secretary Bob Ainsworth told the BBC equipment did not "come from Marks and Spencer" and took time to procure.
He also said there were "some difficult decisions to take" in the coming months over Britain's role in Afghanistan.
He could not put a time limit on Britain's commitment, but wanted to see "significantly more progress in the next year or so", he said.
The government was aiming to speed up the training of Afghan soldiers - from 2,000 a month to 4,000 - which would allow the Afghan army to reach its target strength by November 2010, ahead of schedule, he said.
Foreign Secretary David Miliband later told the Labour Party conference the way to defeat the Taliban was to "separate the hard core from the rest".
Mr Miliband added that at present, ordinary Afghans "don't know who is going to win, and so don't dare give us all the backing we need".
The UK currently has about 9,000 military personnel in Afghanistan - the second largest deployment of any nation - and Mr Ainsworth said he would only consider increasing that if "other nations step up to the plate".
In his conference speech, Mr Ainsworth accused the Conservatives of "ignoring the facts" about the supply of equipment and vehicles to personnel.
Earlier Mr Brown told BBC Political Editor Nick Robinson that the case for being in Afghanistan was "as strong as it was in 2001".
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