The constant stress of going from contract to contract each year and spending precious time applying for research grants finally took its toll.

Dr Saunders left his contract work at the Garvan Institute in Sydney last year to get a full time job as a lecturer in medicine at the University of NSW, where he still conducts research.

A new report by Professionals Australia has found that only one in five medical researchers are permanent full-time employees.

And more than half expect to vacate the field within five years because of uncertainty around funding for their research.

"The main reason I left the medical research sector was job security," Mr Saunders said. "As you get a little bit older and have a family the concept of going year to year on a contract starts to wear a little thin after a while. I'm sleeping better at night now."

Dr Saunders, who has two young children, was forced to "shelve" his cutting edge pancreatic cancer research because of a lack of funding when it was receiving international attention.

"There are cures being left on the shelf because people are leaving the system," he said. "Some projects require bigger thinking than a two or three-year time frame."

Dr Saunders said he has known colleagues who have continued their research for no money because of their dedication.

A new report by Professionals Australia shows the best and brightest scientists are leaving their jobs because of uncertainty of funding for medical research. The report, which surveyed 314 researchers last year, found nine in ten would be encouraged to stay if they had greater job security.

Professor Doug Hilton, president of the Association of Australian Medical Research Institutes, said people have left the sector because of the uncertainty of funding "and they are really talented people".

"It reduces morale for those who remain and saps energy and creativity. The community wants us to make discoveries that save lives and give hope."

Professor Hilton said job insecurity had particularly impacted on women with caring responsibilities. The survey report, Best and Brightest Advancing Medical Research, found more than three-quarters of people said women were under-represented at senior researcher level.

Chris Walton, the chief executive of Professionals Australia, said medical research institutes could not offer employment security because "they are stuck in a funding merry-go-round".

"That's a handbrake on innovation because of insecure employment, and it's little wonder many researchers are considering their future," he said.

Mr Walton said the federal government needed to provide recurrent funding for medical research institutes so they could attract and retain the best scientists.

"If this government is serious about innovation and medical research – two things they say are priorities – they will end the uncertainty for medical research institutes in this federal budget," Mr Walton said.

"It's ridiculous that we give recurrent funding to hospitals which treat disease, yet we won't properly fund research to prevent, diagnose and treat diseases such as cancer, Alzheimer's and heart conditions."

Health Minister Sussan Ley said there was a "glaringly obvious" gulf in medical research funding when the Coalition was returned to government.

"We set out plans in our first budget to establish the Medical Research Future Fund, which aims to double annual investment in medical research once fully established, eventually injecting an additional $1 billion each and every year," she said.

"The fund sits alongside the Turnbull Government's innovation & science agenda and will distribute $400 million into new research over the next few years, over and above standard NHMRC grant funding.

"This is an important policy to help drive domestic investment and jobs growth and in stark contrast to Labor,which repeatedly tried to cut funding to medical research when it held power."