CSIRO staff are calling for a pay rise of 3.5 per cent a year.
CSIRO staff will have less than a month to bargain over their new agreement before their old accord expires.
Negotiations will start on July 21 even though the agreement was supposed to expire on August 16.
Staff will go into the talks asking for an agreement which ensures contractors and labour hire workers do not undermine their jobs and calling for a pay rise of 3.5 per cent a year.
The CSIRO Staff Association said it had been asking management since November for talks to start and sent an update to members saying management's position remained largely a mystery.
The association told members "some worrying signs have begun to emerge".
"There are indications that management seem keen to embrace a regressive agenda favoured by the federal government that encourages stripping enforceable protections from agreements, making deep cuts to working conditions, curtailing representational rights and cutting real wages," the association's update said.
"Most controversially, some senior managers have made the bald statement – often directly to the faces of staff currently making massive sacrifices – that the impact of government’s cuts to CSIRO jobs and research would not be taken into account when it comes to enterprise agreement negotiations."
The association described the bargaining delay as creating a "near impossible time frame".
"There’s a real risk that CSIRO employees will be financially disadvantaged due to management’s tardiness," the update said.
The government's bargaining framework released in March did not support back pay.
The staff association's bargaining position, released last year, asked for back pay if an agreement was not struck by next month.
The association will be negotiating for a 3.5 per cent a year pay increase, unless other better conditions outweighing this were added elsewhere in the agreement.
The staff union was pushing for superannuation contributions paid to many staff to increase from 9 per cent to 15.4 per cent.
It also called for non Australian staff or those employed on 457 visas to receive payments for health care and education costs
"Payments are currently made in some cases, but CSIRO has complete discretion – very little equity or transparency," the association's bargaining position said.
"Many staff on 457 visas receive inadequate support, particularly in relation to liaison with other government organisations."
A CSIRO spokesman said the organisation had been working with staff and unions since late last year in preparation for negotiating about the new enterprise agreement and issued the required notice of representational rights to staff to start bargaining in June.
"The new government bargaining policy sets out the parameters for bargaining for new enterprise agreements across the Commonwealth public sector," the CSIRO spokesman said.
"The policy applies to all Australian Public Service (APS) and non-APS agencies – including CSIRO.
"We have commenced negotiating with staff in good faith."