The Environment Secretary and Brexit campaigner said the UK pressed Brussels for more flexibility over fisheries during the transition period which will last from exit day in March 2019 until the end of 2020.
Instead the UK will be “consulted” on the allocation of quotas.
Mr Gove urged disgruntled Tories to instead focus on the “significant prize” on offer after the transition, insisting the country would then become “an independent coastal state deciding who can access our waters and on what terms for the first time in over 40 years”.
Taking back control of fisheries policy was a symbolically important issue in the referendum campaign.
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.”
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, several Tories voiced concerns while the DUP, which props up Mrs May’s minority Government, criticised the deal.
Influential Brexiteer Jacob Rees-Mogg will join a Fishing For Leave protest outside Parliament on the Thames today but will leave it to colleagues to throw “prime fish” into the river before Prime Minister’s Questions, in protest at the concession.
Mr Rees-Mogg told LBC radio: “I’m not throwing fish anywhere. I am not a fish-thrower.”
Yorkshire representatives also voiced their concerns, including Halifax MP and shadow fisheries minister Holly Lynch, who told The Yorkshire Post: “The reality is he very personally committed a great deal to the hard and fast line that we were leaving the Common Fisheries Policy and taking back control from the get-go of leaving the European UNion, he personally has misled people.
“He’s either been unable to deliver that in negotiations, which was never in his thinking up until now, or he’s not been honest about Government position and policy has been on this.
Kingston upon Hull North MP Diana Johnson asked Mr Gove in the Commons: “The future of the fishing industry is a politically sensitive issue in Hull and Ukip have talked about a fishing fleet being re-established in Hull.
“But wasn’t one of the main promises made to the people of Hull that we would retain our territorial rights around fishing from day one and isn’t that a promise thats been broken to the people of Hull?”
Penistone and Stocksbridge MP Angela Smith called for a guarantee that fish processing will not be sacrificed in exit talks.
She said her father was a deep sea fisherman in Grimbsy, adding: “So I know it’s one of the hardest jobs in the world