A senior Catholic archbishop has warned he is "deeply troubled" by Australia's vaccine deal with AstraZeneca, saying the potential vaccine uses a fetal cell line that creates an "ethical quandary" for Christians.

Sydney Archbishop Anthony Fisher penned a letter also signed by Anglican and Greek Orthodox religious leaders to Prime Minister Scott Morrison outlining concerns of some Christians over the vaccine's apparent use of a cell line derived from an elective abortion performed decades ago.

The letter, seen by AFP, calls on Morrison to ensure that if the vaccine being developed by Oxford University researchers is rolled out in Australia it is not made mandatory.

It also urges him to pursue other "ethical" vaccine candidates to ensure religious objectors have a choice.

Australia last week announced a deal with AstraZeneca to manufacture the "promising" vaccine if it is proven safe and effective, with plans to offer it for free to the entire population.

Morrison initially suggested it should be made compulsory for its 25 million citizens with an exception on medical grounds before reversing his position.

Fisher, writing in the forthcoming edition of Catholic Weekly, says he believes it would not be unethical to receive the vaccine "if there is no alternative available" but adds he is "deeply troubled by it".

"I'm a strong advocate of vaccinations and not just for COVID-19 as long as they are safe and ethically obtained," he adds.

In 2017, the Vatican's Pontifical Academy for Life decreed that vaccinations "can be used with a clear conscience" and doing so "does not signify some sort of cooperation with voluntary abortion".

A government spokesperson told AFP that Morrison himself a devout Christian "respects the views of Australia's many religious communities and understands the issues that are being raised".

"The government is investing in research and technology that we hope will produce a range of vaccines that will be suitable for as many Australians as possible," the official said.

Among those is the University of Queensland's vaccine candidate, which the official said does not contain fetal cell lines and has received Aus$5 million in government funding.

It is currently in Phase 1 efficacy trials, while the Oxford vaccine is among a handful globally that have reached Phase 3.

The Australian government estimates that up to 95 percent of the population would need to be immune to the virus for it to be eradicated.