The prime minister implored children to stay in class rather than protesting things that "can be dealt with outside of school".
"Each day I send my kids to school and I know other members' kids should also go to school but we do not support our schools being turned into parliaments," Morrison told parliament on Monday.
"What we want is more learning in schools and less activism in schools."
Morrison furiously reacted to Greens MP Adam Bandt during question time about the protest, dubbed the Big School Walkout for Climate Action.
Hundreds of Australian school students are vowing to put the books away and converge on MP offices and parliaments around the country this Friday.
Morrison began his answer to Bandt's question by saying climate change is a "very real and serious issue" that demands attention.
He said the government was acting on climate change through initiatives such as the emissions reduction fund and the renewable energy target.
"We are committed to all of these things, but I will tell you what we are also committed to - kids should go to school," Morrison said.
Bandt said he had met with some of the students involved and backed their actions.
"The PM is unbelievably out of touch with young people, not only in Australia but around the world," he said.
“These students want a leader to protect their future, but they got a hectoring, ungenerous and condescending rebuke from someone even worse than Tony Abbott."
Australian Youth Climate Coalition spokesperson Laura Sykes said Morrison had shown "irrational outrage" to students who care about their education.
"It was shocking see our prime minister condemning students as young as eight, who are sacrificing a day of schooling to stand up for a safe climate future," Sykes told AAP.
"When young people try to have a voice in politics, Scott Morrison is shutting them down, yet he's happy to listen to the coal lobby and big corporations who continue to profit from making climate change worse."
Events are planned in all capital cities, along with about 20 regional areas.