The result of the ballot by the 1750 unionised employees in the Health and Safety Executive will be know by 1 March.
Richard Hardy, a Prospect negotiator, said: "We have been in talks with the executive since May 2003 and management knows our position. We have made it clear that our members are not prepared to make any further compromises when the deal they are being offered amounts to a pay cut over the next three years."
The union is seeking a 2.6% pay increase, which it says the executive can afford, given that the Treasury last year gave the HSE a 3.7% increase in its budget.
Prospect says the offer tabled by the employer is least favourable to the most experienced staff, who are being offered 0.5% a year until 2006.
The union argues that this will have a detrimental effect on pay and pensions, lead to an exodus of experienced staff and compromise the safety of Britain's workers.
Hardy said: "This is not just about levels of pay but about the HSE's ability to maintain an experienced and committed workforce in order to deliver safe workplaces for all."
The HSE declined to comment.