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"So the ultimate responsibility for fighting fires is the state premier's," Kelly said.
But Morgan's co-host Susanna Reid interrupted, saying "but it's a national emergency isn't it?".
"You'd expect the national leader to take charge and not fly out of the country," she added.
Kelly responded saying the only thing a national leader could do was basically wait until he got a response from state premiers asking for more resources.
"Or he could show leadership," Reid said.
Morgan chimed in with, "the truth is he was absent when the fires were burning".
IgnoringKelly's attempt to spruik Morrison's announcement on Monday of $2 billion for bushfire recovery efforts, Morgan continued.
"Scott Morrison thought the right response to these fires erupting in Australia was to go lie on a beach in Hawaii and that was a dereliction of his duty as leader of Australia," Morgan said.
"You're facing right now one of the greatest crises you've ever faced and there is you, Mr Kelly, with respect, a senior politician who still doesn't think this has anything to do with a heating up planet, nothing to see here, nothing to worry about," Morgan said.
Kelly has denied there is a link between climate change and drought, and has slammed students who marched for climate change action last year as "sheep" who are being "manipulated".
"I follow the science" Kelly interjects, as Morgan continues: "as virtually your entire country is eviscerated by fires, it's quite extraordinary".
Kelly responded saying: "Not at all, this is a terrible disaster, this is one of our nation's worst natural disasters … in the past when we had these in our nation … we all sat back and did what we could to fix it up rather than people get out there to score political points."
But Morgan cut his comments short, saying "we have to leave it there".