As far as the U.S. can tell, Gates said, Iran's support for the insurgency is "pretty limited."
Gates noted that he had a public exchange of barbs with Iranian President Mahmoud Ahmadinejad this week over which country is doing harm in Afghanistan.
"We think Afghanistan should have good relations with all of its neighbors, but we also want all of Afghanistan's neighbors to play an upfront game in dealing with the government of Afghanistan," Gates said Wednesday.
In a press conference with Afghan President Hamid Karzai in Kabul on Wednesday, Ahmadinejad responded that it was the United States that was playing a "double game."
"They themselves created terrorists and now they're saying that they are fighting terrorists," Ahmadinejad said.
Gates was in Afghanistan for three days this week. He spoke Thursday at a military base that is home to an Air Force refueling and surveillance operation serving the war in Afghanistan.
The Pentagon asked press traveling with Gates not to name the base.