"I think we're going to get him," Mr Rumsfeld said at a Pentagon press briefing on Thursday.
The defence secretary said the newspaper had misinterpreted his intended meaning, and that he was merely making the point that he could not know in absolute certainty that Bin Laden would be found.
Mr Rumsfeld had told USA Today newspaper that it would be "very difficult" to capture or kill Bin Laden.
"He's got a lot of money, he's got a lot of people who support him and I just don't know whether we'll be successful," he had said, adding that Bin Laden's militant network would carry on without him regardless.
"If he were gone tomorrow, the same problem would exist," he said.
Tough targets
The BBC's US State Department correspondent, John Leyne, says that in his comments to USA Today Mr Rumsfeld appears to have wandered off his script.
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Our correspondent says that while the US administration is keen that the success of its war on terrorism should not be judged by the hunt for Bin Laden, capturing or killing him does remain a key aim.
Mr Rumsfeld did predict that Afghanistan's Taleban rulers would be toppled and there would be a "post-Taleban Afghanistan".
US commanders have admitted that Afghanistan's Taleban rulers - who are sheltering Bin Laden - are proving "tough" opponents, and correspondents on the front lines say Taleban morale remains high after four days of regular US bombing.
US aircraft have continued to attack Taleban positions, including areas where they confront the forces of the opposition Northern Alliance.
The BBC's Kate Clark in Shomali, north of Kabul, says the bombing has hit infrastructure targets but the Taleban have not collapsed and their forces appear to be relatively intact.
Northern Alliance walkie-talkies picked up a Taleban soldier singing a song mocking the forces ranged against him even as the US bombs rained down, she says.
Earlier, the Pentagon admitted it was taken aback by the tenacity of the Taleban as the US-led bombing campaign continued into its third week.
"I'm a bit surprised at how doggedly they're hanging on to power," said Rear Admiral John Stufflebeem.
In other developments: