Michael Gove said he was disappointed with the European Union over its stance on fishing as he faced Tory discontent about the Government's deal with Brussels.
The Environment Secretary, a prominent Brexit campaigner during the referendum, said the UK pressed Brussels for more flexibility during the implementation period after the country has formally left the bloc in March 2019 but the EU would not give ground.
The Government has insisted it has agreed "specific safeguards" with Brussels over the annual fishing negotiations in 2019 but a series of Tory MPs publicly expressed their frustration at the deal.
Taking back control of fisheries policy was a symbolically important issue in the referendum campaign and the Government has come under pressure for not securing that ability from March 29 2019 when the UK leaves the bloc.
Mr Gove told the Commons: "There is disappointment in fishing communities - I know, as someone whose father was a fish merchant, whose grandparents went to sea to fish, I completely understand how fishing communities feel about this situation at the moment.
"I share their disappointment."
He added: "Our proposal to the EU was that, during the implementation period, we would sit alongside other coastal states as a third country and equal partner in annual quota negotiations - and in making that case, we did so after full consultation with representatives of the fisheries industry.
"We pressed during negotiations to secure this outcome and we're disappointed the EU was not willing to move on this."
But he said the text from Brussels' original proposal has been amended and provides "additional reassurance", with the UK's share of quotas not changing during the implementation period and a commitment it can attend international negotiations.
And he added that there was a "significant prize" at the end of the implementation period.
He said: "In December 2020, we will be negotiating fishing opportunities as a third country, an independent coastal state deciding who can access our waters and on what terms for the first time in over 40 years."
In a sign of Tory unease about the reaction to the deal, Theresa May met MPs with fishing ports in their seats to explain the Government's approach.
But in the Commons, a series of Conservatives stood up to voice their concerns.
Douglas Ross said: "There's no way I can sell this deal in the transitional period as anything like a success to fishing communities in Moray, Scotland or the UK."
Former Cabinet minister John Redwood said Mrs May must tell her fellow leaders at this week's European Council summit that the deal is "unacceptable", adding: "We voted to take back control of our fish, our money, our borders and our laws."
Berwickshire, Roxburgh and Selkirk MP John Lamont said he, like many fishermen across Scotland, felt "very badly let down by this deal because we're not going to be taking control of our waters as quickly as we had hoped".
Jacob Rees-Mogg, chairman of the influential European Research Group, has warned Mrs May that the concessions made to Brussels will only be acceptable if they result in a "proper Brexit".
The DUP - which props up Mrs May's minority administration in Parliament - also hit out at the terms of the agreement.
The party's Brexit spokesman Sammy Wilson said: "There will be many people who will be alarmed and concerned about this particular agreement."
Mrs May told her Cabinet that the deal reached in Brussels represented "another step forwards on the road to Brexit".
Around the Cabinet table senior ministers discussed the "safeguards which are in the agreement to protect the interests of British fishermen".
Asked when Mrs May would consider the UK to have taken back control of its waters, the Prime Minister's official spokesman told reporters: "It's clear what is going to be happening going forward in the implementation period.
"In December 2020 we will be negotiating fishing opportunities as a third country and an independent coastal state for the first time in over 40 years."
The spokesman added: "As we leave we will be taking back control of our waters and this period will allow us to develop arrangements for fishing that can create a more financially self-sufficient, profitable and responsive UK seafood sector."