The Department of Health has been emailing prospective donors in recent days saying funding for the Leave for Living Organ Donors program - which pays kidney and liver donors up to nine weeks' leave at the minimum wage, or about $6000 - will cease on June 30.

The letters tell donors that if they want the subsidy they have to undergo surgery before July and lodge their claims by September.

The letters have stakeholders worried that the successful four-year-old program - started by Labor but extended by the Coalition in 2015 - will be cut as part of new Health Minister Greg Hunt's savings drive.

Kidney Health Australia CEO Mikaela Stafrace said she was concerned about the program's future.

"The program helps alleviate the financial stress that is often be experienced by living organ donors," she said. "We estimate that to keep it funded up until 2021 will cost less than $1.5 million."

More than 100 Australians accessed the program in 2016, helping more than a third of the 267 people who made living kidney donations.

Mr Hunt initially confirmed current funding was due to finish on June 30 and it was being re-assessed as part of the budget process, however he later said: "I am very confident there will be a very positive announcement in the near future."

Greens leader Richard Di Natale wrote to Mr Hunt last week calling on him to ensure funding is continued.

"Donors require a significant time away from work to recover from the surgery, and this program provides access to funding to ensure that they are not out of pocket as a result of their decision to help save a life," Senator Di Natale said in his correspondence.

"The scheme provides a level of support to the admirable Australians who choose to become live donors.

"Indeed, removal of the scheme could create a disincentive for those who would otherwise become donors."

Living organ donors are typically relatives or close friends of people who have end-stage kidney disease or liver failure. Because of long recovery times, donors often exhaust their employer-provided leave or are forced to take leave without pay.

The government said the program is not an incentive to donate but rather a means of properly supporting people who have already made the decision.