He's part of growing chorus of Republicans who are seizing on the Democratic front-runner's comments and trying to paint her as out of touch on one of the biggest government scandals in recent years.
Clinton told MSNBC's Rachel Maddow on Friday that issues within the VA have "not been as widespread as it has been made out to be."
McCain, who spent 5 1/2 years as a POW during the Vietnam War, said the facts say differently.
"I don't know what Hillary Clinton's view of what 'widespread' is but facts are stubborn things," the 2008 Republican presidential nominee said on a conference call with reporters.
McCain also took issue with Clinton's claim that Republicans have made the VA partisan and want to use it to privatize the VA. In doing so, McCain noted that he worked with her Democratic rival, Sen. Bernie Sanders, to pass a VA reform bill.
"Now Hillary Clinton, in her blind ambition, has injected partisanship into the VA issue and that is disgraceful," he said. "She owes an apology."
Rep. Jeff Miller, chairman of the House Committee on Veterans' Affairs, was also on the call. "Hillary Clinton really proved she has no idea what she is talking about on veterans issues," he said.
Clinton's campaign on Tuesday backed away from the candidate's claim that issues at the VA were not "widespread."
Brian Fallon, Clinton's press secretary, acknowledged to CNN wait times and other mismanagement of care by the Department of Veterans Affairs were indeed "systemic" and that Clinton will roll out her plan to reform the VA in November.
"Even now, too many of our veterans are still waiting an unacceptably long time to see a doctor, or to process disability claims and appeals," Fallon said in a statement to CNN.
Fallon said that when Clinton is president she "will work to further reform the VA to make sure it truly works for our veterans, and will demand accountability and performance from VA leadership."
Veterans groups fired back
at Clinton earlier this week.
Fallon said Clinton's comment on MSNBC is being "misinterpreted" and that he hopes to clarify her position.
"(Hillary Clinton) will work to further reform the VA to make sure it truly works for our veterans, and will demand accountability and performance from VA leadership," he said.
But Paul Rieckhoff, founder and CEO of the Iraq and Afghanistan Veterans of America, or IAVA, called her comments a "head-scratcher."
"That is not a winning argument -- or factually correct," he tweeted.
Republican presidential candidates have also weighed in. Former Florida Gov. Jeb Bush said in an interview that aired Wednesday that Clinton's comments were "a direct affront" to veterans.
"This should be the first priority of our government to take care of the men and women in uniform that have served us so heroically, (who) come back home and then get mistreated by their own government," he said on Fox News. "It is outrageous. She's wrong."
Florida Sen. Marco Rubio blasted the former secretary of state on Saturday while campaigning in Greenville, South Carolina. He said the VA is one of the most frequent issues that constituents ask his office for help with and accused Clinton of being "out of touch."
"People talk about this," he said at an event hosted by Concerned Vets for America, which is backed by the Koch Brothers. "I don't know where she's getting her information, but she's out of touch ... not designed to deal with 21st century issues that face vets."
A VA inspector general concluded inappropriate scheduling practices at VA medical centers were "systemic" in 2014, after a CNN investigation revealed veterans
were dying while waiting for care on "secret" lists at the Phoenix VA. The scandal led to the resignation of then-VA Secretary Eric Shinseki.
A more recent CNN investigation found the problem is actually getting worse -- veterans continue to wait months for care at some VA facilities, and a September federally funded report concluded the agency remains "plagued" by problems including growing bureaucracy, staffing challenges and unsustainable costs.
Fallon said on Tuesday that despite the issues "the VA provides unique and critical services and innovative care to our veteran community."
Clinton "does not believe that privatization will solve the problems that the VA is facing. Rather, it must deliver high-quality care while acting as an integrated payer-purchaser and facilitating a full range of services for all veterans, regardless of where they live," he said.
Clinton's position on privatization is similar to Vermont independent Sen. Bernie Sanders, her top rival for the Democratic nomination. Sanders joined with McCain in 2014 to pass a VA reform bill, one of the biggest legislative achievements of his career.
But it wasn't just GOP opponents knocking Clinton for her comments. A Tuesday editorial in the Arizona Republic declared
, "The last thing vets need? Presidential aspirants playing partisan politics with their predicament."
"Ideological preferences may frame what reformers recommend to fix the VA's troubles. The conservative Concerned Veterans for America, for example, advocates rolling back the vast bureaucracy's mission. Many Democrats, meanwhile, advocate substantial increases in spending," the editorial said. "But no one has injected the kind of accusatory, issue-dismissing language into the debate that Clinton has."