Legislation to set up the government's $20 billion medical research future fund has passed the Senate after the coalition made several amendments.

The Abbott government's $20 billion medical research future fund has cleared the Senate despite concerns about the potential for its funding decisions being politicised.

The government says the fund will be the largest of its kind in the world, firming Australia's position as a world leader on medical research.

It made 20 amendments to its legislation, including stronger controls over how the money will be distributed, meaning it must go back to the House of Representatives for approval.

In a joint statement on Wednesday, the treasurer and health and finance ministers said the fund will receive an initial contribution of $1 billion from the uncommitted balance of the previous Labor government's Health and Hospitals Fund.

Remaining contributions will come from budget savings in health that have passed or will pass the parliament, with the first $10 million to be distributed from the fund this budget year.

Labor said the government has now made more than 40 amendments to the "shoddy and sloppy" legislation in both the lower and upper house.

The original legislation included no independent, peer-reviewed oversight of where money will be distributed, opening the possibility of it being used to pay for coalition election projects, said opposition health spokeswoman Catherine King.

A Labor government will amend legislation to have the fund administered by the National Health and Medical Research Council (NHMRC), she said.

"Labor welcomes the passage of the bills through the Senate but remains concerned that they still do not appropriately ensure significant funding decisions are not politicised," Ms King said.

A Senate inquiry into the legislation last week heard the fund could be hijacked by special interest groups tugging on politicians' heartstrings.

Phoebe Phillips, president of the Australian Society for Medical Research, said there needs to be a compulsory peer review process before money is allocated to projects, so money is not just handed to the "loudest speaker".

The federal government says the recommendations of the inquiry, and suggestions from the Greens, have been incorporated into the legislation.

The fund will be administered by an eight-member independent expert advisory board - including a seat for the chief executive of the NHMRC - to be announced shortly.

The health minister will also be legally required to report to the parliament every two years on how the distributed money has met the strategies and priorities independently set by the board.