The chief medical officer contracted by the Australian government to look after the health of refugees and asylum seekers on Nauru is being deported from the island.

Fairfax Media has confirmed with government sources that senior doctor Nicole Montana will be placed on a flight to Australia later on Wednesday and replaced. Other sources suggested Dr Montana was arrested by Nauruan authorities on Tuesday but it was not clear why.

In a statement issued Wednesday morning, contractor International Health and Medical Services said Dr Montana was sacked on Tuesday for "breaching the rules" at the Australian-funded regional processing centre in Nauru.

"The IHMS senior medical officer was stood down on 16 October 2018 for a breach of regional processing centre rules. She is departing Nauru today," IHMS said.

"A replacement senior medical officer is already in Nauru [and] there has been no impact on the services provided to transferees."