According to the Washington Post newspaper, which received leaked details of the briefing by the Rand Corporation, an independent think-tank, Saudi Arabia was accused of supporting terrorism.
The Rand Corporation reportedly told a Pentagon advisory body in its 10 July briefing that the US should punish Saudi Arabia if it failed to stop supporting Islamic extremism.
"It did not represent the views of the government, it did not represent the views of the Defence Policy Board," US Defence Secretary Donald Rumsfeld said.
Mr Rumsfeld also told Pentagon workers that the public disclosure of such briefings was clearly harmful.
A Pentagon spokeswoman said that neither the presentation nor the advisory board members reflect the official view of the administration, which regards Saudi Arabia as a long-standing ally.
The advisory board brings together some heavy-weight former officials, including Henry Kissinger, James Schlesinger and Newt Gingrich - and is chaired by Richard Perle, a leading advocate of a US military attack on Iraq.
Emerging tensions?
Mr Rumsfeld said Saudi Arabia was like any other country with a broad spectrum of activities, some of which the US did not agree with.
The BBC's Pentagon correspondent, Nick Childs, says Mr Rumsfeld's remarks betray some of the strains which have undoubtedly emerged in the US-Saudi relationship in the past year.
He made mention of the fact that a number of the hijackers involved in the 11 September attacks on US targets were Saudis, and that Saudi Arabia is wrestling with these issues.
Our correspondent says there have been frustrations in parts of the US defence establishment over the extent of Saudi support for recent US military and diplomatic campaigns.