Staff at the Department for Environment, Food and Rural Affairs and its agencies are staging a one-day strike over "unfair" pay gaps.
Salaries for similar jobs vary by thousands of pounds
The PCS Union said more than 5,000 had joined walk-outs in England and Wales, but Defra said it was fewer than that.
The PCS claims pay gaps between people doing similar jobs average £2,010, and is calling for "greater pay coherence".
Defra said agency staff pay had fallen behind core workers' salaries and that it was in talks to resolve that.
The strike on Friday involves union members from the department (Defra), and its associated agencies, the Rural Payments Agency (RPA) and the Centre for Environment Fisheries and Aquaculture Science (Cefas).
The union said picket lines would be formed at all their main sites, including London, Exeter, Bristol, Newcastle and York.
It complains that separate pay negotiations mean, for example, that an administrative officer's starting salary in Cefas is £11,474, compared with £15,221 in the RPA.
General Secretary Mark Serwotka said: "Defra and its executive agencies are a prime example of the unfair and farcical nature of civil service pay.
"Members doing the same job have had enough of the growing inequality of pay within the department and its agencies and want to see people doing the same job paid the same rate."
PCS is calling for a single set of negotiations to cover the department and its agencies.
But a Defra spokeswoman said: "A return to central pay bargaining in Defra is quite simply not in our gift.
"It has been government policy since 1996 that departments and agencies have been delegated responsibility for setting pay and terms and conditions to suit their own business needs."
She admitted salaries for agency workers had fallen behind those for core Defra staff in the last four years.
The department was talking with the agencies and unions on developing "coherent arrangements" on pay, she said.