The House Budget Committee chairman "believes the integrity of our generals and admirals is unimpeachable," Ryan spokesman Conor Sweeney said. "They serve our country with distinction and unparalleled honor."
His comments Thursday came hours after Ryan told a Washington budget-policy forum, sponsored by the National Journal magazine, that senior U.S. military commanders didn't really want the $614 billion budget request they presented to Congress.
"We don't think the generals are giving us their true advice," Ryan told the forum. "We don't think the generals believe that their budget is really the right budget.
"I think there's a lot of budget smoke and mirrors in the Pentagon's budget."
The Pentagon's new U.S. defense strategy calls for a shift in the reach of the Navy and Air Force to the Pacific, but Ryan said its budget "doesn't do that. So I think the strategy doesn't match the budget because I think what is going on here is this is a budget-driven strategy not a strategy-driven budget."
Pentagon press secretary George Little said Defense Secretary Leon Panetta "expects honest, straightforward input from our military leadership and he believes that is precisely what they do on a regular basis, time and time again."
Defense officials testifying before Congress must solemnly swear to give their best military advice.
Rep. Adam Smith, D-Wash., the top Democrat and second-most-senior member of the House Armed Services Committee, called on Ryan to apologize for suggesting U.S. generals were dishonest in endorsing the Pentagon budget.
"And if he won't, [House] Speaker [John] Boehner [R-Ohio] and Republican leadership should condemn Ryan's remarks," he told the National Journal.
"Calling our senior generals and admirals, like [Chairman of the Joint Chiefs of Staff Martin] Dempsey, 'liars' is totally out of bounds," Smith said.
"You may not agree with everything they say, but accusing them of bowing to political pressure and lying to Congress about national security is an insult to them and the brave men and women they command on behalf of our grateful nation."
President Barack Obama and congressional Republicans agreed on a budget Aug. 2, 2011, calling for defense cuts of $487 billion over a decade, as Washington ends the wars in Afghanistan and Iraq, and attempts to reduce the nation's deficit.
Those defense cuts were included in Obama's $3.8 trillion 2013 budget proposal released Feb. 13.
Ryan's alternative $3.5 trillion 2013 budget plan, proposed March 20, passed the House 228-191 Thursday. It would let the military budget grow with inflation over 10 years.
An additional $500 billion in defense cuts could go into effect next year unless Congress stops them. The cuts are part of $1.2 trillion in across-the-board cuts that could be triggered by the Budget Control Act of 2011, which Obama signed Aug. 2, intended to end an era of trillion-dollar deficits.
The Pentagon said Thursday it anticipated hundreds of thousands of layoffs in the defense industry if lawmakers failed to reverse the $500 billion in cuts.