The growing civilian toll had prompted the Afghan government to seek new rules of military engagement by international troops.
In a report released by Human Rights Watch, a US-based group, at least 119 civilians were killed in air raids in the first seven months of 2008, mostly in US-led operations.
The defence secretary's visit also comes at the time of a series of controversial cross-border raids on Pakistan by US forces.
"I think what we have seen and I have been pleased about, is in recent weeks to see the Pakistani army once again putting pressure in this area.
"It is my hope that we can work closely with the Pakistanis to prevent this from being a safe haven that threatens both Afghanistan and a democratic Pakistan," Gates said after meeting Hamid Karzai, the Afghan president.
"In addition to the forces our international partners have agreed to send, we will be sending additional forces in 2009, and my expectation is we will be able to meet the requirements the commanders have in the course of 2009," he said.
General David McKiernan, the senior US commander in Afghanistan, said on Tuesday that he needed more than 10,000 combat troops in addition to those already committed. The US had announced an increase of 4,500 soldiers for Afghanistan early next year.
There are currently at least 33,000 US troops there, with a similar number provided by other international forces.