Rural Payments Agency (RPA) chief executive Mark Grimshaw has announced he is to stand down after more than six years in the job.
Mr Grimshaw has been the target of severe criticism and has been held responsible for late BPS payments, with some farmers still waiting for their 2015 claims to come through.
Last November, a committee of MPs asked whether successive government ministers were right to declare their confidence in Mr Grimshaw's leadership at the end of a year of missed payments targets and inaccurate settlements.
Responding to MPs who questioned whether ministers’ faith in him was justified, Mr Grimshaw said: “They are absolutely right to have confidence in me as I believe this committee should have confidence in me as well, mainly because there is no one in this country that understands the Bsic Payment Scheme, the history or the payments system that we have got in place better than I do.”
The RPA has also come under repeated criticism from House of Commons Select Committees over the past few years for failures in its CAP-D IT project to automate payments of CAP money to farmers and rural businesses.
Due to problems with the RPA's IT system, some farmers have waited over 16 months between payments that should come yearly, and coupled with low farmgate prices for produce this has caused significant hardship for many farmers and farming groups.
Environment Secretary, Andrea Leadsom said: "In the six months that I have worked with Mark I have been grateful for his clear commitment to resolving outstanding BPS issues. Both he and Paul Caldwell have worked hard to achieve a strong recovery from the challenges of the first year of this new system.
"The agency remains fully focussed on paying all remaining eligible claims as quickly as possible including those outstanding from 2015."
Mark Grimshaw said: "After six years at the helm I have decided now is the time to stand down and hand over the reins to a new leader to take the organisation through the next phase of its development as part of the Defra Group."
Paul Caldwell has been announced as the incoming Interim Chief Executive of the RPA.