Speaking to reporters at a Pentagon news conference, Gates called the internal administration discussions about a troop build up "a very constructive, deliberative process."
He said he thought it was "appropriate" that new administration carefully weigh the issue before acting, saying "this is the first time this president has been asked to deploy a large number of troops overseas."
A senior defense official said Feb. 4 that it would probably be several weeks before the administration rolls out its long-term strategy in Afghanistan. But Mr. Obama has been seen as very likely to approve a request from the top commander in Afghanistan for three more U.S. combat brigades numbering roughly 14,000 troops.
"The options before him gives him several" choices, including whatever would be the pace of the build up, Gates said.
He said that expected drawdowns of troops in Iraq will lessen the strains the military services have been feeling while fighting in both Iraq and Afghanistan.
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"I actually asked about possibly changing the policy at Dover probably a little over a year ago" during the Bush administration," Gates said. "The answer that I got back, partly as a the result of contacts with the families, was that if the news media were at Dover, many of the families would feel compelled to be there for the services of their fallen family member."
Gates said there were privacy concerns and said that some families would face financial hardships in traveling to the air base for a ceremony honoring the dead.
"I have asked that we review it again and we will do so," he said, "and I've put a fairly short deadline on that."
"If the needs of the families can be met," Gates added, "the more honor we can accord these fallen heroes, the better."
Police spokesman Wazir Pacha said the attack in Khost province was carried out by a suicide bomber in a vehicle. But the NATO spokesman blamed the attack on a roadside bomb.
The majority of NATO troops in Khost, which border Pakistan, are American, though the spokesman for NATO's International Security Assistance Force would not confirm the troops' nationalities. The spokesman asked not to be identified because he was not the media office's lead spokesman.
Taliban bomb attacks have risen sharply over the last three years as the militant force has intensified its insurgency campaign against U.S. and NATO troops.
Either way, the critical comments coming from the new administration signal an end to the era of special relationship that the Afghan leader enjoyed with former President George W. Bush.
A new tension is evident. In a news conference Tuesday, Karzai said the discord is like a "gentle wrestling" match - and he hopes Afghanistan ends up on top.
Karzai is seen as having one of the world's most difficult jobs - directing Afghanistan's rise after the Taliban destroyed the government and ruined relations among the country's various ethnic groups.
But the job has gotten much tougher lately.
Mr. Obama said Monday that Afghanistan's government seems "very detached from what's going on in the surrounding community." Secretary of State Hillary Clinton recently called the country a "narco-state." And a new poll found that 40 percent of Afghans think their country is headed in the right direction, down from 77 percent in 2005.
Karzai has vowed to seek re-election in August.