A child in Victoria who authorities feared may have contracted Ebola has been cleared of the having the deadly virus.

The one-year-old recently returned from West Africa where an outbreak of the deadly viral infection there has already killed more than 2,000 people.

When the child was taken to the Frankston hospital in Melbourne's south-east on Friday with diarrhea, doctors feared the worst.

Authorities activated the state's Ebola response plan and the child was transferred to the Royal Children's Hospital in the CBD where he was placed in isolation.

Victoria's Health Minister David Davis said it was the state's first suspected case and the first opportunity to test the response plan.

"It was managed in accordance with the state's plan, the Royal Children's Hospital managed the case," he said.

"It was found to not be a case of ebola virus and the patient was discharged."