Liverpool City Council is working with the UK Health Security Agency (UKHSA) after two children from the same school died.
Millstead School in Everton, which teaches children with special educational needs and disabilities, has been dealing with an outbreak of the Giardia infection.
But the UKHSA said the common gastric disease was unlikely to be the cause of the deaths.
Emma Savage, consultant for the UKHSA's Cheshire and Merseyside health protection team, said investigations were ongoing into cases of the illness.
She said: ‘We have provided information and advice to the school and parents. Public health measures have been put in place to help prevent further cases.’
The school’s headteacher, Michelle Beard, said: ‘The entire Millstead School community is devastated to have learned of the sad recent passing of two of our younger children.
‘We have sent our sincerest condolences to both of their families.
‘Both children filled their classes with joy during their time with us, and they will forever be in our hearts.’
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