The letter to Scott Morrison is signed by the Greek Orthodox Archbishop of Australia Makarios, the Catholic Archbishop of Sydney Anthony Fisher and the Anglican Archbishop Glenn Davies.
Dr Davies has also warned that he is likely to boycott the vaccine the prime minister will make freely available to everyone. Mr Morrison has announced that Australia has signed a letter of intent with AstraZenaca to purchase 25 million vaccines if the trials are successful.
The archbishops' concerns are centred around the use of cell lines from an electively aborted foetus.
The letter, which was publicly released on Monday, described the harvesting of foetal tissue as "deeply immoral" and warned members of their leaders' congregations may decide to refuse the vaccine.
Jewish, Hindu and Islamic leaders in Australia say they would welcome the Oxford University coronavirus vaccine if it is successful, despite other religious leaders raising ethical concerns over the use of cell lines from an electively aborted foetus.