General Peter Pace said on Thursday that while the US needs to get its message out to the Iraqi people, Pentagon programmes should be reviewed so readers will know what to believe.
"I think there are ways to get your message out, but get it out in a form that people understand how the message got there," said Pace, chairman of the Joint Chiefs of Staff.
"They need to know that, so they can make their own judgment about what they believe and don't believe in the article. The worst thing you can have is people feeling like somehow they've been snookered."
Critics have said the practice contradicts American values of freedom of the press.
At a Pentagon news conference on Thursday, Donald Rumsfeld, the secretary of defence, said he expected the department to review its policy on whether it is acceptable for the military to pay journalists to run stories provided anonymously by the US military.
He declined to state his view of the practice.
"We want the United States to be seen for what it is: An open society that supports free press not only at home but overseas. To the extent that our operations bring that into question, we should review how we're doing it"
General Peter Pace, chairman,
Joint Chiefs of Staff
"I said we'd take it under advisement and take a look at it. I'm not going to take a judgment off the top of my head," Rumsfeld said.
The investigation was opened after US newspapers reported that a Washington-based contractor paid Iraqi newspapers to run hundreds of stories written by US military information operations officers in Iraq.
Pace's remarks seemed to take a different tack from comments earlier this month by General George Casey, the US military commander in Iraq.
Casey ordered an initial review of the programme which found that the Lincoln Group - a private company that was used to plant the stories to hide the fact they originated from the US military - did not violate its contract with the military.
Casey said he had no plans to stop the practice.
The army also was reported to have paid Iraqi reporters through a Baghdad press group to write favourable stories.
Pentagon officials have defended the programme as a necessary tool in the "war on terror", saying it is critical to get an accurate message out to the Iraqis about what the US is doing in their country.
Pace said the policy should be reviewed because, "we want the United States to be seen for what it is: An open society that supports free press not only at home but overseas".
"To the extent that our operations bring that into question, we should review how we're doing it."