The Labour leader was speaking during two days of official engagements in the region accompanied by shadow secretary of state Louise Haigh.
Reflecting on having worked in Northern Ireland for six years with police in the early 2000s, Sir Keir said he learned the importance of trust and the role of the UK Government as an honest broker, bringing communities together.
There are tensions over the Northern Ireland Protocol, with unionists claiming the additional checks on goods are placing a border down the Irish Sea.
There have been demonstrations against the Protocol as well as legal challenges to it.
Sir Keir told the PA news agency in Belfast that Boris Johnson had “not been straight about the consequences” of the Protocol.
“He is now pretending it is someone else’s problem, and in Northern Ireland that won’t wash,” he said.
“There has to be a practical way forward on this, I think there is a practical way forward if the parties are flexible and negotiate, but the most important thing is trust.
“There is a positive future here but it does require the British Government to properly understand its role, and I think that this Prime Minister, Boris Johnson, has betrayed the people of Northern Ireland by not properly honouring that (the UK Government being an honest broker), and the words that have been used in pretty well every meeting I have had here in Northern Ireland is a lack of trust in the Prime Minister as an honest broker.
“That is a massive missing piece.”
Sir Keir visited Forge Integrated Primary School in Belfast on Thursday morning before meeting Police Service of Northern Ireland Chief Constable Simon Byrne at police headquarters in the city.
The Labour leader later met with the five main political parties at Stormont.
He said the Good Friday Agreement and its promise of peace must “never be taken for granted”.
“Returning to Northern Ireland today, I can see how much is still at stake,” he said.
“The peace here was built on the trust, courage and commitment of the communities of Northern Ireland and political leaders. I felt that while working here in the years after Good Friday. And it is with those values in mind that I will go into today’s important meetings.
“This morning, I saw the transformation that peace helped bring about at an integrated school in Belfast. I saw the smiles of hope from young people as they look to the future. Whether we are in Westminster or Stormont, as political leaders we owe it to that generation to deliver on the promise of the Good Friday Agreement.
“We must recognise that trust is fragile, and progress is stalling. I understand the concerns of communities and businesses here about the problems with the Northern Ireland Protocol. I’m here to listen and to call for serious, practical solutions.”
Sir Keir heard the concerns of the five parties, including opposition to the Protocol from unionists.
Speaking to media after the meetings, Sir Keir said trust in the Prime Minister was at an “all time low” in Northern Ireland.
He said the UK negotiating a deal on veterinary standards that could reduce the needs for checks in the Irish Sea would be “a big step in the right direction”.
Ms Haigh said they discussed such a deal with all the parties, adding there was “relative consensus that is part of the solution”.
“It’s not the only thing but ultimately we need to see the British Government getting back round the negotiating table with the European Union and using the mechanisms of the Protocol to find that agreement,” she said.
“It is not a sustainable solution to keep proposing unilateral mechanisms and unfortunately that’s what we anticipate will happen in the next couple of weeks from (Brexit minister) David Frost.
“We need to see the consensus and that trust to find sustainable solutions for Northern Ireland.”
The Irish government has said an agreement on SPS (sanitary and phytosanitary), similar to that between Switzerland and the EU, could eliminate 80% of checks.
Sir Keir and Ms Haigh went on to meet with victims of the Troubles on Thursday evening.