Prime Minister Scott Morrison claims government agencies have told him "hundreds" of people on Manus Island and Nauru would be flown to Australia "within a matter of weeks" if Labor and the crossbench pass a bill giving doctors more say in treating sick refugees.

The claim, made in a letter sent to Bill Shorten on Monday urging the Opposition Leader against voting for the proposed law, was swiftly rejected as "scare tactics" by doctors and advocates.

The bill to compel ministers to more readily approve medical transfers of refugees to hospitals in Australia is expected to come to a vote when Parliament resumes next week. If passed, it would be the first serious defeat of a government in the House of Representatives in 90 years.

In a bid to avert defeat, Mr Morrison on Monday proposed a new panel of medical experts to advise the government on transfers but that offer failed to dent support in Parliament for the bill proposed by independent MP Kerryn Phelps.

Dr Phelps' legislation limits the discretion of the minister to intervene when two doctors recommend treatment on the mainland. The immigration minister of the day would have to approve the transfer unless he or she "reasonably believes" it would harm security, as defined by the Australian Security Intelligence Organisation Act.