About 3,000 members of the Public and Commercial Services union have walked out on the six-month anniversary of the foot and mouth outbreak, demanding parity in pay after what they claim are years of being the "poor relation of the civil service".
They say there will be further strikes next week if pay demands are not met.
When the Ministry of Agriculture, Fisheries and Food (Maff) was merged with a part of the Department of Environment, Transport and the Regions (DETR) to create Defra in June, former Maff employees quickly realised that they were being paid up to £4,400 less than their colleagues from DETR.
According to the union, an ex-Maff administrative officer in London makes £10,500 on average, while an ex-DETR administrative officer makes about £14,000.
Union negotiator Sheila Pickman said: "PCS members have endured years of low pay in comparison with other government departments, and Maff's failure to address that has led to the very stark contrasts now within Defra.
"Many clearly find it easy to hurl criticism at Maff/Defra's handling of crises but they seem to forget that behind the titles are huge numbers of poorly-paid people working extremely hard in very stressful situations."
Ms Pickman said that if today's strike did not result in an offer of pay parity, the union would conduct targeted walkouts in regional offices next week.
The most recent government pay review awarded Maff officers an extra £1,000 per year in London and £700 in the regions.
Mike Dalton, a branch co-secretary in the PCS and a Defra employee, said that the pay offer amounted to an extra 26p per hour.
An unimpressed Mr Dalton said: "You can't even buy a postage stamp for that, but it was imposed so we can't really reject it."
He said the situation came to a head on Friday afternoon, when employees received a notice stating that if industrial action continued, holiday may be restricted or curtailed.
He said that about 100 union members from his office in Cambridge were on strike today.
Ms Pickman added: "The government cannot create these departments and fail to deal with the problems. We hope the Treasury will see the sense of what we are doing."
Officials from Defra were not available for comment this morning.
