With about 132,000 troops in Iraq, Gates said there were constraints as to how many extra troops could be sent to Afghanistan at least until after Iraq’s elections in January.

“I would say also that the availability of forces is still a challenge,” he told a news conference on Thursday.

Referring to plans to reduce US troops in Iraq over the next year, Gates said that “until the more accelerated drawdown in Iraq begins after the elections there … it will be a challenge for us.”

The military also was limited by efforts to increase the time soldiers spend back at home between combat tours, he said.

The defense secretary’s comments come amid intense speculation that the top US and NATO commander in Afghanistan, General Stanley McChrystal, is preparing to make a case for more troops in the fight against the Taliban and allied insurgents.

President Barack Obama already ordered an additional 21,000 troops to Afghanistan ahead of the country’s August 20 elections and the number of US forces is set to reach 68,000 before the end of the year.

There are also some 30,000 international troops under NATO command in Afghanistan.

Asked why US forces were not sent in earlier to southern Afghanistan, where thousands of Marines have deployed over the summer, Gates said: “The forces weren’t available to send in until fairly recently. We got them in there as fast as we could.”

Gates said he and the chairman of the Joint Chiefs of Staff, Admiral Mike Mullen, had told McChrystal that “we want him to ask for what he thinks he needs.”

“And I think you have to allow your commanders that freedom,” he said.

But he repeated his concerns about too big of a US military “footprint,” saying it was important not to alienate Afghans who currently view the NATO-led coalition as “their partner.”

“I just worry that we don’t know what the size of the military presence might be that would begin to change that.

“And I think we need to move with considerable care in that respect and in close consultation with both our allies, but especially with the Afghans and the Afghan government,” Gates said.

McChrystal, who is drafting an assessment of the Afghan war effort that is due to be submitted by early September, is under pressure to seize the initiative from the Islamist insurgents amid anxiety in Congress about an open-ended US mission.

Obama has sought to shift the focus to the Afghan mission but has had to balance competing demands from the commander in Iraq, amid warnings the situation there remains fragile.

Describing a “mixed picture” in Afghanistan, Gates said he could not predict how long US troops would have to stay, saying there were too many uncertainties.

“In some parts of Afghanistan, the Taliban have clearly established a presence,” he said.

But Gates said the insurgents could be defeated “in a few years” while economic and civilian aid efforts represented a “decades-long enterprise.”

General James Cartwright, the vice chairman of the Joint Chiefs of Staff, said at the same press conference that the military was looking closely at how to combat improvised explosives, which were the main cause of casualties among NATO-led troops.

“That’s one area that we’re going to have to focus in on,” Cartwright said. Countering the explosives might require a change in tactics or “additional resources,” he said. “We’re going to have to take a serious look at that.”

Civilian analysts who advised McChrystal last month on his assessment have called for moving troops out of fortified bases and having them mingle more with the local population in a bid to win the trust of Afghans.

McChrystal is also reportedly considering focusing more on securing cities and towns instead of devoting resources to manhunts for Taliban or Al-Qaeda militants.

Gates acknowledged that McChrystal was considering shifting troops away from remote areas to population centers.

“I suspect that may be something that’s addressed in the general’s assessment,” he said.