Walney School in Barrow-in-Furness shut last month after reports that about 20 students had been bitten by what were believed to be harvest mites.
Pupils returned to the school this week but the council confirmed that part of the roof may now have to be replaced.
A Cumbria County Council spokesman told the North West Evening Mail: “Despite investigations by the council, Public Health England, Barrow Borough Council Environmental Health and pest control contractors, neither the source nor the species of insect responsible for the bites has been proven.
“The council has also been unable to identify any other turf roofed buildings that have been linked to this type of problem.
“However, the report by Public Health England has identified the roof as one plausible source, amongst others.
“Our over-riding priority in this situation has always been to return the school to normality as soon as possible.
“In light of the available evidence, we are currently considering two options: intensive treatment of the turf roof covering or its removal.
“Removal would be an interim arrangement to eliminate it from the on-going investigation.
“We must be very clear about the costs, timescales and impact on the school of each of these options.”
Scaffolding will be erected today to give authorities full access to the roof to allow them to make a final decision about the next course of action.
Eric Wright was main contractor on the £6m school extension which opened 18 months ago.