There has been community concern about their return from Sinai, particularly after it was revealed some of the locals who had been working with the troops have tested positive for Covid-19.
But health minister Ifereimi Waqainabete said they're being held in strict quarantine and will be tested for the coronavirus.
"Because this is a big group - the numbers are big - they are using up two facilities I believe," he said.
"But before they can finally go home, the soldiers will have to be tested again and they have to be Covid-19 negative before they can be released to go home."
Mr Waqainabete said every measure was being taken to ensure there's no threat to the public.
The military said all steps had been taken by the government, as well as Australia - who flew the soldiers home - and the Multinational Force and Observer Mission to minimise the soldiers' exposure.
The soldiers' 12 month deployment had already been prolonged because of rapid border closures in March, which made a repatriation difficult.
They will be held in isolation for two weeks, and will be released to their families after then if they test negative for the coronavirus.