Two children tested for Ebola in Melbourne on Thursday after returning from a trip to West Africa have been cleared of the potentially fatal disease.

Victoria's Deputy Chief Health Officer, Professor Michael Ackland, said the girls aged 4 and 8 years old are being treated for a respiratory illness and are doing well.

Professor Ackland said the siblings returned to Melbourne overnight with their parents and another sibling following an extended visit to Guinea.

The other family members are well.

"Routine screening of returning travellers from Ebola-affected countries in west Africa identified that the girls had elevated temperatures," Professor Ackland said.