Church schools want the government to postpone the withdrawal of face masks in schools until the end of May.
In a statement on Monday, the schools said they currently have to contend with a "record number of sick students and staff" and worry that going mask-free would result in classes "ending up without teachers."
A spokesperson explained the position further.
"Church schools are concerned that more staff will become COVID-19 positive, with the consequence that children will have to remain at home due to a lack of educators," she said.
The schools' statement comes just two days before children will be allowed to take their masks off.
As of Thursday, face masks will no longer be obligatory in schools, accelerating a change that was due to come into place after Easter holidays.
Students have had to wear masks inside classrooms since 2020, when the masking rule was first introduced.
Church schools suggested some alternatives to their end-of-May request: if authorities were unwilling to shift the mask-free date back, then each school should be permitted to decide for itself when masks could come off.
And if that option was also not considered, the government should allow students and staff to remove masks in outdoor areas such as grounds, playing fields, and other open spaces, "while retaining the mandatory use of masks in classrooms and other indoor spaces."
They said that while they were in favour of the eventual removal of masks in classrooms, their use had proven effective at controlling the COVID-19 pandemic in schools.
"Therefore, considering that students often spend up to six hours a day together in the same room, this should be the last measure to be withdrawn."
As of Monday, there were 9,134 active COVID-19 cases in Malta - the highest amount since mid-January. Authorities insist few of those cases are acute, but are no longer publishing data about the number of virus patients requiring hospital treatment.