The Ear Bus is run by Telethon Speech and Hearing.
Opposition Health Spokes-man Roger Cook quizzed Health Minister Kim Hames on the apparent funding cut, but Dr Hames said there was no suggestion from him or his staff that the funding should not continue.
Mr Cook called on Dr Hames to guarantee funding so the southern metro service could continue.
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READ NOW‘I am not providing a guarantee because I have not made the decision,’ Dr Hames said in Parliament.
Mr Cook said cancelling the Ear Bus program would set back efforts to improve Aboriginal health and literacy.
‘The prevention of glue ear not only stops debilitating health problems, it helps them hear, pay attention in school and get an education.’
Ear Bus Foundation chief executive Paul Higginbotham said the foundation was interested in taking over the service and would see if the department would offer the contract for tender.
‘It’s a very needy area of the metro area and schools like Challis are high need,’ he said.
A spokeswoman for Telethon Speech and Hearing said the organisation was still contracted to provide ear health services at select schools within the eastern metropolitan area and the South West.
Telethon Speech and Hearing offers Aboriginal Health teams that provide ear health services from babies and children aged to five years in Maddington, Bentley, Hilton and Kwinana.