After he declined the political meeting, requested amid growing tensions over post-Brexit restrictions, Ms O’Neill, Sinn Fein’s deputy leader, refused to meet him at all.
However, Mr Johnson was to hold a meeting with First Minister and DUP leader Arlene Foster during a visit tied to the response to the coronavirus pandemic.
He also joined Health Minister Robin Swann, the Ulster Unionist Party leader and Mrs Foster at a vaccine centre in Lakeland Forum in Enniskillen, which is in her Fermanagh and South Tyrone constituency.
Mrs Foster urged the Prime Minister to “stand up for Northern Ireland” and ditch the “intolerable” protocol governing Irish Sea trade post-Brexit, which has angered unionists who say it undermines the nation’s place in the UK.
In a statement, Ms O’Neill said: “Mary Lou McDonald and myself have a long-standing request to meet with the British Prime Minister to discuss a number of commitments which he and his Government have reneged on in the New Decade New Approach over this past year, and also his reckless and partisan approach to the Irish Protocol. He did not facilitate the meeting.
“I have no plans to meet with him today.”
Mr Johnson said he was willing to meet people all the time.
He added: “Alas, Michelle was otherwise engaged.
“I am always happy to meet all sides.”
Ms McDonald criticised the “most unfortunate” manner of the Prime Minister’s visit.
Speaking to reporters on Friday, she said: “I have to say that the manner in which this visit was planned and conducted was really most unfortunate.
“We have for some time now been seeking a meeting with Boris Johnson. We have very substantial and important matters to discuss with him.
“The British Government is in default in respect of key commitments that it has made.
“Unfortunately he has not facilitated that meeting.
“He did meet with the leader of the DUP, who suggested that we might cooperate in a photo-op in Belfast, but that was never going to happen.
“We have serious business to transact with Boris Johnson, so we will be reaching out to Downing Street again, and seeking that meeting without further delay.”
Sinn Fein MP John Finucane said the party was refusing to engage with the “day out for unionism” after No 10 refused the request for a “professional, grown-up engagement” to cover topics including the Northern Ireland Protocol.
Mr Finucane, who represents North Belfast, said: “We’re not in the business of engaging in a fairly superficial PR stunt, which is what the British Prime Minister invited us to do today.
“We have made the request to meet with him. I think it’s insulting to the 770,000 people on this island who vote for us that he feels it appropriate to ignore and refuse that meeting.”
The Prime Minister’s official spokesman said: “Michelle O’Neill was invited to join the PM on the visit.”
The protocol was agreed by the EU and UK during the withdrawal negotiations to prevent a hard border on the island of Ireland.
It achieves that by keeping Northern Ireland in the EU single market for goods, with regulatory checks and inspections now required on agri-food produce moving into the region from the rest of the UK.
The new arrangements have caused some disruption to trade since the start of the year as firms have struggled with new processes and administration.