Johnson appeared on CNN's "New Day" and told host Chris Cuomo, "I have the deepest respect for John McCain and in no way was I trying to criticize him."
"If anything, I was trying to defend his position," Johnson said.
The Wisconsin senator said he had reached out to McCain and hoped to talk to him Thursday.
Cuomo asked Johnson if he believed McCain was "on his game," to which the senator replied "absolutely."
"I was just expressing sympathy for his condition," Johnson said. "He's not impaired in any way, shape, or form."
Johnson stunned a local Wisconsin radio host Wednesday when he brought up McCain's brain tumor during a discussion on the GOP healthcare bill.
"Again, I'm not gonna speak for John McCain - he has a brain tumor right now - that vote occurred at 1:30 in the morning, some of that might have factored in," Johnson said.
"Really?" replied one of the radio hosts, saying McCain recovered from surgery on a blood clot near the tumor and "flew all the way out to Washington, DC."
"You really think that played a factor in his judgment call?" the host asked.
"Again, I don't want to speak for any senator," Johnson said. "I really thought John was going to vote 'yes' and send that to conference at 10:30 at night and by about 1:00, 1:30, he voted no. So you'd have to talk to John about what was on his mind."
In a statement Wednesday, a McCain spokesman said it was "bizarre and deeply unfortunate" that Johnson would question McCain's judgment.
"Senator McCain has been very open and clear about the reasons for his vote," the statement said.