The UK will regain full control over the country's fishing waters for the first time in 40 years after December 2020, Michael Gove has insisted.
The environment secretary said he shared the "disappointment" of fishing communities who hoped this would happen on Brexit day, 29 March 2019.
But Mr Gove urged them to keep their "eyes on the prize" of getting control.
Lib Dem Alistair Carmichael, who raised the issue, said "the mood in fishing communities is one of palpable anger".
The fishing industry had wanted the UK to regain full control over the country's fishing waters on Brexit day, 29 March, 2019.
Instead the deal will see the UK "consulted" on quotas with the situation remaining largely unchanged until 2021.
Mr Gove said the government had pressed for the UK to be an equal partner in fishing negotiations during the 21-month "implementation period" - but the EU had blocked this.
"We were disappointed the EU would not move on this," he told MPs, saying that the UK only had to wait a further year for complete control of its waters.
"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," he said.
"It's important that all of us, in every area, accept that the implementation period is a necessary step towards securing that prize.
"For our coastal communities it's an opportunity to revive economically, for our marine environment it is an opportunity to be managed sustainably and it's critical that all of us - in the interests of the whole nation - keep our eyes on that prize."
But Mr Carmichael replied: "I have to tell you, if you don't already know it, the mood in fishing communities is one of palpable anger - this is not what they were promised."
He added that if the government can "let us down like this over a deal for the transitional period, how do we know they will not do it again when it comes to the final deal?"
The SNP's Stephen Gethins asked the minister to say "at what point our fishermen became a bargaining chip", adding: "Or has that been the case all along?"
Mr Gove replied: "For a party that has raised grievance to an art form, you have a damn cheek making that case."
Former Tory minister John Redwood pressed him to go back to the EU and say "this deal is unacceptable".
Mr Gove said: "We didn't get everything we wanted, but... it's the view of this government that we need to make sure this implementation succeeds to get the greater prize at the end of it."
Prominent Eurosceptic Tory Jacob Rees-Mogg said he was "slightly concerned" by Mr Gove's tone in relationship to negotiations that the European Commission "would not allow us something in a negotiation".
Mr Gove said the implementation period would allow the government to prepare "for all the benefits Brexit will bring".
The Commons exchanges came as Scottish Conservative MPs who held talks with the prime minister on fishing said she "reassured" them the UK would take control of its waters after the transition period.
Alister Jack, the MP for Dumfries and Galloway, said he felt assured by Mrs May's comments but John Lamont, the MP for Berwickshire. Roxburgh and Selkirk, warned: "The government should be clear that they are on notice - no deal for fishermen, and they will have to think again on the terms of our departure."
The Daily Telegraph reported that Tory critics of the deal are planning to protest on a boat on the Thames by Parliament on Wednesday.
Scotland's First Minister and SNP leader, Nicola Sturgeon, claimed the concession made to the EU in the transitional period was "shaping up to be a massive sell-out of the Scottish fishing industry by the Tories".
Labour's shadow fisheries minister Holly Lynch said it was "understandable" fishing communities felt "angry and let down".
Bertie Armstrong, head of the Scottish Fishermen's Association, accused the EU of asking "for the bargain of a lifetime" by seeking to keep the UK under Common Fisheries Policy rules for "as long as physically possible".
Compared with Iceland, which is allowed to keep 90% of fish caught in its waters, the UK keeps 40% under the Common Fisheries Policy, he told BBC Radio 4's Today programme.
But Niel Wichmann, head of the Danish Fishermen's Association, said the transition period "is a sensible agreement which gives us time - a couple of years - to work out how we keep our fishing stocks sustainable, how we keep our fisheries sustainable after Brexit".
Recap: The deal announced on Monday
On Monday, the EU's chief negotiator Michel Barnier said the legal text of the agreement for the 21 months after Brexit marked a "decisive step" but added that it was "not the end of the road".
The key aspects of the agreement announced in Brussels are:
- The transitional period will last from Brexit day on 29 March 2019 to 31 December 2020
- EU citizens arriving in the UK between these two dates will enjoy the same rights and guarantees as those who arrive before Brexit. The same will apply to UK expats on the continent
- The UK will be able to negotiate, sign and ratify its own trade deals during the transition period although they can only come into force from 1 January 2021
- The UK will still be party to existing EU trade deals with other countries
- The UK's share of fishing catch will be guaranteed during transition but the UK will, in effect, remain part of the Common Fisheries Policy, yet without a direct say in its rules, until the end of 2020
Other aspects of the post-Brexit relationship yet to be agreed include what happens to the Northern Ireland border in the longer term.