Mr Howard told a joint parties meeting that several MPs have spoken to him about the issue since cabinet decided to maintain a ban on therapeutic cloning for stem cell research.
His announcement that a conscience vote on the issue would be allowed comes only a day after he abandoned the government's planned tough immigration legislation, when it became apparent the bill's passage in the Senate appeared doomed.
Australian Democrats Senator Natasha Stott Despoja is planning a private member's bill on the research, similar to the one that overturned the federal health minister's control over the abortion drug.