More than 900 staff have been cut from Defra in 2016 following budget cuts.
The number of people employed at Defra fell to 21,964 at the end of March 2016 from 22,875 a year earlier.
Despite calls for more investment following the winter flooding, 232 staff have been cut in water and flood risk management.
Nearly 600 staff were lost in the executive agencies, which includes the Rural Payments Agency (RPA).
In the government’s autumn spending review, it was announced Defra faced budget cuts of 15 per cent by 2020.
In the report, Defra permanent secretary Clare Moriarty said they have laid the foundations to’ transform the Defra group into a modern, streamlined organisation.’
She acknowledged the difficulties faced over the past year describing the Environment Agency’s response to the flooding as ’public service at its best, with local rescue services and the military working together with our teams to support people and communities who were flooded.’
She also said the RPA had faced ’major challenges implementing CAP farm support payments.’
"The decision to switch to paper claims mitigated the impact of delays in IT system development but many farmers received payments later than in 2014," she said.
"I am very conscious of the impact this had on farmers already experiencing difficult economic conditions."
The report claimed that since the spring of 2015, a firmer control has been taken of delivering essential requirements for the Basic Payment Scheme (BPS) and payments have been successfully made on time to the majority of farmers.