Administration officials have said that Russia's airstrikes in Syria this week are not targeting ISIS. The administration said the attacks have been "indiscriminate" and have included rebels fighting Syrian President Bashar al-Assad's administration.
Asked about that perspective Friday on Fox News, Rubio said the attacks were actually quite discriminate and targeted.
"That's absurd," Rubio said of the White House's claim. "Vladimir Putin is deliberately targeting all the non-ISIS rebels. The more moderate they are, the more he's going to target them."
Rubio said it was part of a Putin strategy to take out anyone who can oppose Assad -- who Russia supports -- so that the rest of the world has no choice but to accept him.
"He's trying to thin out the opposition so that the only opposition left in Syria to Assad is ISIS, and at that point he'll be able to force world to support Assad," Rubio said. "I don't understand why the White House doesn't see it and why the President and his administration don't understand that."
Rubio is set to give a foreign policy address on Friday about Russian aggression. He has been showing off his foreign policy credentials on the campaign trail as a member of the Senate Foreign Relations Committee.
A missing piece of U.S. strategy, he said, is to try to counteract the information warfare that is sowing distrust of America among civilians on the ground, something Putin is strategically taking advantage of.
"He's been very cunning about it," Rubio said, adding the White House has been "quite frankly, incompetent about it."
Opinion: Putin's Syria moves leave U.S. looking weak
Other candidates on both sides of the aisle called for the U.S. to establish no-fly zones in Syria to stop the bombings.
"I personally would be advocating now for a no-fly zone and humanitarian corridors to stop the carnage on the ground and from the air," Democratic front-runner Hillary Clinton said Thursday in an interview with Boston's WHDH.
And Ohio Gov. John Kasich echoed that idea on Friday. If elected president, he said he would not tolerate any violation of that zone by Russia.
"Do not violate the no-fly zone. Enter that no-fly zone, you're going to have to accept the consequences," Kasich said from a New Hampshire press conference.