"The health advice has been consistent that for children, schools are a safe space for children," he said.
Classrooms across the country have been moving increasingly towards remote learning, as states and territories respond to the coronavirus pandemic.
Mr Morrison said it was important classrooms remained open, especially for children of essential workers and others who cannot be effectively homeschooled.
He also said he wanted his own kids to get back to school to be taught in a classroom by a teacher as soon as possible.
"That's what I want to see happen," he said.
"When a school in New South Wales says that they go to can deliver that for them, I will happily have them back there in a heartbeat."
Mr Morrison admitted there was some confusion about whether it was also safe for teachers to be at school, but said the health advice was that "teachers are more at risk in the staffroom" than they would be in a classroom with children.
He said "proper arrangements" needed to be in place to ensure they can be safe in their work environment.
'State and territory issue'
Mr Morrison said while the national cabinet agreed to a set of guiding principles, the running of state schools was a "state and territory issue" and Australians should listen to leaders in their jurisdictions.
"I want to make that clear, (the) Commonwealth does not run state schools," he said.
"If you are going to school in Victoria there is only one person you need to listen to and that is the Premier of Victoria."
In Victoria, term two for schools resumed on Wednesday with most students learning from home.
NSW Premier Gladys Berejiklian has said she wants to see a gradual increase towards face-to-face teaching during the term.
Queensland will review its advice on schools by 15 May.
The 'National Principles for School Education response to COVID-19' released by the Prime Minister's Office contains seven pieces of advice.
The first states education is "best delivered by professional teachers to students in the classroom", but the second conceeds the "remote delivery of education services" may be needed during the COVID-19 crisis.
Schools must remain "healthy and safe environments for students, teachers and other staff", according to the third.
The fourth principle outlines that state and territory governments and non-government sector authorities are responsible for managing and making "operational decisions" for schools, subject to funding agreements with the federal government.
The fifth point states decisions regarding the response to COVID-19 in the schooling sector must continue to be informed by expert, official, national and state-based public health and education advice.
The sixth says all students must continue to be supported by their school, while the seventh reiterates medical advice that going to school represents a "very low health risk to students".
People in Australia must stay at least 1.5 metres away from others and gatherings are limited to two people unless you are with your family or household.
If you believe you may have contracted the virus, call your doctor (don’t visit) or contact the national Coronavirus Health Information Hotline on 1800 020 080. If you are struggling to breathe or experiencing a medical emergency, call 000.
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