Environment Agency chairman Sir Philip Dilley has quit after coming under fire for not returning from a family holiday in Barbados during the recent floods.
He said the decision to resign was because "expectations of the role have expanded to require the chairman to be available at short notice throughout the year", something he felt was "inappropriate".
He insisted he was "well qualified" to carry out the role but media scrutiny on him was "diverting attention" from efforts to help those affected by flooding.
Sir Philip took responsibility for the statement put out by the Environment Agency (EA) that said he was at home, when he was with his family in the Caribbean.
In his resignation statement he said: "I want to be clear that I have not made any untrue or misleading statements, apart from approving the statement about my location over Christmas that in hindsight could have been clearer."
Setting out the reasons behind his decision to quit, Sir Philip said: "My reason for resigning is that the expectations of the role have expanded to require the chairman to be available at short notice throughout the year, irrespective of routine arrangements for deputy and executive cover. In my view this is inappropriate in a part-time non-executive position, and this is something I am unable to deliver.
"Furthermore the media scrutiny focused on me is diverting attention from the real issue of helping those whose homes and businesses have flooded, as well as the important matter of delivering a long-term flood defence strategy.
"This same media attention has also affected and intruded on my immediate family, which I find unacceptable."
He insisted that the EA was an "extremely competent and well-run organisation" and he retained "the full support of the board".
Environment Secretary Liz Truss, who accepted Sir Philip's resignation, said: "He has ably led the Environment Agency through some challenging times and leaves it a much better organisation, as shown in its excellent response to the recent flooding which saw staff working around the clock to protect and help thousands of people across the country.
"It is important that the Environment Agency continues to have a strong leadership team and its chief executive Sir James Bevan will continue his excellent work heading up the operational and day-to-day running of the organisation."
Current deputy chairman Emma Howard Boyd will become acting chairman with immediate effect, Ms Truss added.
Sir Philip had faced demands to quit from MPs in some of the parts of northern England left underwater during his Caribbean break.
Tory MP for Ribble Valley Nigel Evans said: "Thousands of people were knee-deep in water on Boxing Day. Thousands more gave up their Christmases to help and are still doing so in the clean-up operation which is still ongoing.
"It was the worst flooding in the north of England in living memory and people thought it was bizarre that the chairman of the Environment Agency decided to stay on holiday.
"I think he has made the right judgment call today."
Liberal Democrat leader Tim Farron, MP for Westmorland and Lonsdale which was also hit by flooding, said: "Many staff gave up their Christmas Eve, Christmas Day and New Year's Eve. Their boss should have joined them.
"It seemed to many that this organisation was bereft of its formal leadership when it was most needed.
"The public deserved better."
Sir Philip will step down from the £100,000-a-year post at the end of January, Defra said.