He said neither of the two extremes - a nationwide counterinsurgency and nation-building effort in Afghanistan nor "walking away from the place" - were do-able.
"The key in Afghanistan is we have got to figure out what is achievable, measured against the legitimate interests of the US, primary among which is al-Qaeda," Kerry said.
"In Afghanistan itself we have to resolve the question of whether the Taliban are per se a threat to us."
In talks on Wednesday between Barack Obama, the US president, and his top advisers on a new strategy for Afghanistan, some aides emphasised the main threat to US interests was al-Qaeda, not the Taliban.
The administration's analysis of the threat posed by the Taliban could play a role in whether Obama accepts part or all of McChrystal's request for extra troops, beyond the 68,000 he has already approved for this year.
Meanwhile, General Jonathan Vance, the chief Canadian commander in Afghanistan, described the military situation as "serious" and "desperate".
"It's a major emergency," he said said in an interview on Canadian televison on Wednesday.
Obama's Afghanistan review has been further complicated by delays to the outcome of the August presidential election in Afghanistan, held up by allegations of widespread fraud that marred the vote.
If the Afghan president Hamid Karzai's share of the preliminary vote, currently 55 per cent against the 28 per cent of his nearest rival, Abdullah Abdullah, falls below 50 per cent after fraudulent ballots are discarded, a run-off will be called for in November.
Tribal leaders in Karzai's Pashtun-dominated southern powerbase said this week they would boycott a run-off, citing disillusionment with the fraud claims, the time taken to declare a winner and a lack of security.
Robert Gibbs, the White House spokesman, said on Wednesday it would "work with whatever government there is" but added having a "strong credible partner is extremely important."
Japan to end help
Japan, in the meantime, said it will end a naval refuelling mission backing the US war in Afghanistan, a month before Obama is due to visit Tokyo.
"I explained that the special law will expire," Akihisa Nagashima, the defence secretary, said in Washington after meeting Obama's security and defence advisers.
Yukio Hatoyama, the counrty's new prime minister who took office last month, has
said he wants "more equal" relations with the US and opposed plans for a new US military air base to be built on southern Okinawa island.