Rove made the remarks at a conference last Thursday that he attended with US President Barack Obama's former spokesman Robert Gibbs, according to the New York Post's Page Six.
"Thirty days in the hospital?" Rove reportedly said.
"And when she reappears, she's wearing glasses that are only for people who have traumatic brain injury? We need to know what's up with that" he added.
Clinton, 66 and the presumptive Democratic front runner for the 2016 presidential race, was admitted to hospital in New York for three days to treat a concussion and blood clot she suffered in the fall, and which prevented her from testifying at the time about the deadly attack on the US mission in Benghazi, Libya.
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Clinton's team quickly rejected Rove's comments.
"Karl Rove has deceived the country for years, but there are no words for this level of lying. As to her health, she is 100 per cent," Clinton spokesman Nick Merrill said.
Several Republicans had assailed Clinton for possibly exaggerating the seriousness of her condition in order to avoid testifying before Congress about the deadly September 11, 2012 attack.
In January 2013, she testified for seven hours about the crisis.
Meanwhile, Clinton is keeping up a breakneck pace of speeches and appearances across the country, and she is preparing a book tour to push her new autobiography which comes out next month.