Speaking at the Pentagon Gates said that he and Admiral Mike Mullen, the chairman of the Joint Chiefs of Staff, had told McChrystal, that "[they] want him to ask for what he thinks he needs", adding "I think you have to allow your commanders that freedom."
But with about 132,000 troops currently 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.
|Nearly 70,000 US troops will be in Afghanistan before the end of the year [EPA]
Gates also repeated his concerns about too big of a US military "footprint," in Afghanistan, saying at the moment, local residents see the coalition of forces 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," he said.
Barack Obama, the US president, has made Afghanistan one of his top foreign policy priorities and has already ordered an additional 21,000 troops to Afghanistan.
That will push the number of US forces in the country to 68,000 before the end of the year.
His administration, however, is struggling on how to refocus on Afghanistan, while withdrawing US troops from Iraq.
In a report released this week, the Senate Foreign Relations Committee warned Obama that unanswered questions about continuing US involvement in Afghanistan could frustrate the public.
"The administration has raised the stakes by transforming the Afghan war from a limited intervention into a more ambitious and potentially risky counterinsurgency,'' the report said.
"These core questions about commitment and sacrifice can be answered only through a rigorous and informed national debate."