A report has found some education programs are underway to help bridge the gap, but they are limited and run without government support.
Ten-year-old Sid Bezwada was diagnosed with leukaemia in February.
He has been out of school for eight months, but not out of touch.
That is thanks to the Back on Track program run by Westmead Children's Hospital in Sydney.
The program provides educational support to cancer patients so they can remotely attend lessons with their classmates and maintain their schoolwork during treatment.
Sid Bezwada says the program has made his chemotherapy much more bearable.
"I get to keep up with my class, and I guess you're not getting bored because you're coming in every day to do some work, so you're not just sitting around mindlessly gazing."
Sid Bezwada's mother, Minnie Puttaya, says she has seen her son's confidence grow during the classes.
"He has been sort of doing his work and enjoying himself, and it's that normality that you're able to maintain in the midst of these rather unusual circumstances."
Programs like the one her son is doing are very rare, with only a few operating in Australia.
That is because they receive no government funding.
A new report estimates around 60,000 children miss school as a result of serious illnesses.
The report has found negative impacts on the students include delayed development, academic underachievement, behavioural problems, increased anxiety and bullying.
The co-founder of the educational advocacy group Missing School Inc, Megan Gilmour, says government is neglecting students with severe, long-term medical conditions.
"Our governments need to properly meet the academic, social and emotional needs of seriously sick and injured kids who are missing school. This is about saving hearts and minds, not just bodies."
Dr Belinda Barton is the department head of the Children's Hospital Education Research Institute at Westmead Children's Hospital.
She says, without educational support, many students struggle to reintegrate into school.
"It's frightening for them to go back if they've missed out on school for two years. They haven't been in touch with their friends. There's a whole new network of friends."
Sid Bezwada says he hopes other children will get the same support he has.
"If they're away from school for two years or one year, it can have a major impact on their schooling, and they could fall behind. So it's good to have this education to keep them up (to date)."
