"I expect by the week's end the secretary will have received General McChrystal's resource request," Morrell said.
"But I want to make it perfectly clear that once he has it, he intends to hold onto it, until such time as the president and his national security team are ready to consider it."
He said it was "simply premature to consider additional resources" until an assessment of the war effort submitted by McChrystal was fully reviewed.
The details of McChrystal's request remain unclear but he is reportedly expected to ask for 10,000 to 30,000 additional troops.
In the commander's own assessment of the war published in the Washington Post on Monday, the general paints a dire picture and warns that without more troops the NAT0-led mission faces failure.
McChrystal, who assumed command of more than 100,000 NATO-led troops in Afghanistan in June, said the campaign in Afghanistan "has been historically under-resourced and remains so today."
Wednesday's announcement at the Pentagon came after US media reported that defense officials had told McChrystal to put off a formal request for reinforcements.
Morrell suggested that by having the troop request sent to Gates, there would be less media attention concentrating on McChrystal's role.
He also denied there was frustration in the US military leadership over the pace of deliberations at the White House and rejected US media speculation that McChrystal would be ready to resign if his request for more troops was denied.
"Just absurd. Absolutely ridiculous," Morrell said.
There are about 65,000 US troops in Afghanistan and the American force is due to reach 68,000 by the end of year.
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