Ziyad Thabit, undersecretary of the education ministry in the Islamist Hamas-ruled enclave, said pupils would follow a remedial curriculum throughout August and classes would be limited to four a day.
"The ministry has prepared a plan based on various scenarios for dealing with the school year," he said.
The United Nations agency for Palestinians, UNRWA, which provides education to hundreds of thousands of children in Gaza, said over 285,000 pupils had returned to its 277 schools.
In a statement, it said it has "put in place preventative measures such as providing all the necessary materials to sanitise schools" and training staff on how to use sanitation materials effectively.
It said it would cancel morning assemblies and keep children in classrooms during breaks to avoid too many pupils gathering in one place at a time.
"The measures will be reviewed once a week and improved as necessary,” UNRWA said.
Around a million people live in Gaza, many of them in poverty and a third of them refugees. The territory has been under Israeli blockade since 2007.
Gaza’s Hamas-run health ministry has reported 78 cases of the COVID-19 illness, with one death.