Khan's jab at Trump was ill-timed, as the Bahamas had just been slammed by Dorian when it was rated a Category 5 storm, Rubio said Tuesday on "Your World."
"I didn't even hear the comment," he said.
"It's irrelevant to me what the mayor of a city halfway around the world thinks. Bottom line is, he should actually be expressing concern for the Bahamas -- which is part of the British Commonwealth -- which has been wiped out."
In an interview with Politico over the weekend, Khan criticized Trump for canceling his trip to Poland to commemorate the 80th anniversary of the start of World War II due to the impending hurricane and instead playing golf at one of his courses.
"He's clearly busy dealing with a hurricane out on the golf course," Khan said.
The president later responded to Khan, calling him "incompetent" and saying former President Barack Obama would too often fly to Hawaii. The course Trump visited is about 30 miles northwest of the White House.
“The incompetent Mayor of London, Sadiq Khan, was bothered that I played a very fast round of golf yesterday. Many pols exercise for hours, or travel for weeks," he said of the politician, who is a member of the left-wing Labour Party.
"Khan should focus on 'knife crime,' which is totally out of control in London... He is a terrible mayor who should stay out of our business."
Speaking with host Neil Cavuto, Rubio said Khan should understand the Trump administration has given Florida everything it has asked for during every hurricane it has dealt with -- and plans to help the Bahamas recover after the storm battered the northern part of the archipelago.
"People can say whatever they want," he said of the president's storm-response critics overall.
"We've had multiple storms under the Trump presidency. He's never said 'no' to anything we have asked for.
"I think no matter who you intend to vote for... this White House has been very supportive of Florida after and before storms."