ABC News and The Washington Post cited unnamed advisers in reporting that Rubio, R-Fla., wasn't on the short list for the No. 2 spot on the GOP ticket.
"I can't imagine who such people are, but I can tell you this: They know nothing about the vice presidential selection or evaluation process," Romney told reporters in Michigan. "The story was entirely false. Marco Rubio is being thoroughly vetted as part of our process."
Earlier in the day, Romney had refused to comment on reports that Rubio, a rising star in Republican politics, wasn't under consideration as a potential running mate.
The presumptive GOP nominee initially told Fox News only that "a number of people are being vetted" but that only two people -- he and a senior adviser -- know who's on the list. He repeated that statement Tuesday evening but clarified Rubio's status as a potential vice presidential pick.
The statement was an unusual departure from the secrecy that has surrounded Romney's process in selecting a running mate. But it speaks, in part, to Rubio's political influence among the Republican base and Hispanic voters.
The flap came on the day Rubio released a memoir and Romney's concluded a six-state bus tour. The Florida Democratic Party blasted a message to reporters titled: "Rubio fails preliminary review in Veepstakes."
Asked about the reports during an appearance on Fox News, Rubio also refused to weigh in.
"I'm not commenting on the vice presidential process," he said. "That's been basically what we've said the whole time because, out of respect for Gov. Romney, the last thing he needs is to have to be addressing questions about this because really the campaign's not about that."
Rubio's exclusion from Romney's short list would disappoint some conservative activists, but it would not come as a complete surprise. While he offers obvious political benefits as a Hispanic leader from the swing state of Florida, Romney advisers have consistently said that Romney would give preference to those candidates with the greatest experience and ability to lead the nation on Day One. It's a reflection both of Romney's philosophy and lessons from the selection of former Alaska Gov. Sarah Palin four years ago as the GOP running mate.
A former state lawmaker, Rubio, 41, has served in the Senate for less than two years. Romney did not address Rubio's credentials Tuesday.
Inexperience also works against other oft-mentioned candidates, including New Hampshire Sen. Kelly Ayotte and New Jersey Gov. Chris Christie.
A handful of more likely picks joined Romney on his bus tour in recent days as part of unofficial public tryouts for the No. 2 spot. Their interactions offered clues about who Romney might choose.
Former Minnesota Gov. Tim Pawlenty traveled on Romney's bus with him for two full days, on Friday in New Hampshire and through Saturday in Pennsylvania. He often warranted his own introduction, with a local official talking up his accomplishments as Minnesota governor before Pawlenty took the stage to introduce Romney.
When Pawlenty left the tour, it was to fly to New York to appear as a surrogate for Romney on ABC's "This Week."
On Sunday, Ohio Sen. Rob Portman and his wife, Jane, went along for the ride. By this time, though, Romney had been joined by a pack of family members -- sons Craig and Matt, and five grandchildren. That left Portman and his wife riding on a different bus from Romney's for part of the day.
Still, Romney's team trusted Portman to talk to the reporters who travel with the likely Republican presidential nominee. A Portman aide snapped BlackBerry photos as the senator did a background briefing.
Less visible was Wisconsin Rep. Paul Ryan, whose role was limited to introducing Republican National Committee Chairman Reince Priebus at an event at a factory in Ryan's hometown of Janesville. Wisconsin Gov. Scott Walker, whose June 5 recall election victory was a big win for Republicans, introduced Romney and accompanied him on a tour through the factory.
Romney's Boston headquarters has been engaged for weeks in the secretive process of weighing the pros and cons of each potential pick.
With less than three months to go until Republican National Convention in August, the campaign has little time to waste as it meticulously prepares the presumptive Republican nominee to make one of his most important decisions. Advisers concede that Romney could make his pick earlier than right before the convention to help boost fundraising efforts.
Knowledge of the process is limited to a few of Romney's highest-level aides. Information is on a "need-to-know" basis -- and as far as those aides are concerned, there are few people inside the Boston headquarters who need to know, let alone reporters and other outsiders.
The process is so secret because it's so sensitive.
A vice presidential vetting is possibly the most intense background check in politics. Everything is fair game: voting records and the political past, to be sure, but also personal issues.
"I think everyone should take a deep breath," Rubio said Tuesday. "Here's the one thing everyone should know: Gov. Romney's going to make a great choice. In that I'm confident."