Workers at the government science body the CSIRO were left reeling on Wednesday after bosses told them another 500 jobs were to go as a result of cuts in Tuesday’s budget.

The organisation’s chief executive Megan Clark warned of “painful” days ahead for scientists, researchers and their families as they face yet another round of cuts.

Dr Clark said another 420 jobs would be culled by the middle of next year, with another 80 full-time positions to probably go in the following years.

The job losses will come as the CSIRO grapples with a funding reduction of $111.4 million over four years, with the organisation also to be hit with a separate "efficiency dividend" cut of $5 million over the forward estimates period.

A recently announced restructure will also see 300 science workers joining the dole queue, with the CSIRO’s Staff Association describing the latest news as “ugly”.

“We will need to reduce the number of staff in CSIRO by up to 420 [full-time equivalent] by the end of June 2015,” Dr Clark said.

“A further potential decrease of an estimated 80 FTE is forecast to occur through to June 2018 dependent on external revenue.

“These reductions are in addition to the previously announced loss of up to 300 FTE arising from our reform program.

“This will be painful for our teams and our people who have dedicated themselves to the future of Australia and their families.”

The CSIRO’s portfolio budget statement revealed more than $24 million had been set aside to pay for the golden handshakes of those leaving the organisation.

Staff Association acting secretary Michael Borgas described the cuts as short-sighted and destructive.

The Australian Climate Change Science Program will be folded into a new National Environmental Science Program, with a funding cut of $21.7 million in the process, in a move the Staff Association said could damage the ability of CSIRO and the Bureau of Meteorology to advise on global warming.

The staff group was also critical of the funding cut to the Co-operative Research Centre program which the union said could result in a significant hit on important research by CSIRO – the largest participant in the centre.

“Cutting funding to CRC’s may damage CSIRO research across the most important sectors of national priority: the environment, agriculture, information and communications technology, mining, medical science and technology and manufacturing,” Dr Borgas said.

“These funding cuts to CSIRO are short-sighted and destructive.

“They will do lasting harm to CSIRO and the capacity to deliver new inventions and crucial research for the next generation of Australians.”