The North Island event was set to take place in Hamilton and the South Island championships in Christchurch on April 4-5.
"We understand that this will lead to disappoint for many of our athletics community, however we fully support the stance of Government and School Sport NZ in the interest the health and well-being of our students, teachers, schools, officials, volunteers, coaches, family members and others in attendance," a statement said.
Water polo and volleyball championships in Auckland and Palmerston North respectively have also been hit.
The decision will be reviewed on April 6.
Events where alternative dates aren't possible will be cancelled.