Northern Ireland’s First Minister Arlene Foster urged Boris Johnson and Michael Gove to “act on” their unionist beliefs.
Mrs Foster also accused the EU of not respecting the sovereign territory of the UK.
Her words come amid tensions after the brief triggering by the bloc of Article 16, with particular ire among unionists in Northern Ireland who are calling for it to be ditched.
The protocol was designed to prevent a hard border with Ireland but has resulted in additional checks for goods crossing from Great Britain to Northern Ireland.
Article 16 overrides part of the protocol which prevents a hard border on the island of Ireland, and was intended as an emergency measure only.
Ms Foster told UTV's Peston: “I believe they [Johnson and Gove] are both unionists but it is important that they act on that now and it is important that they realise that part of the United Kingdom is being treated differently.
“And actually if you look at the protocol it talks about respecting the fact that the sovereign territory of the United Kingdom as one, it also talks about respecting the internal market of the United Kingdom.
“I don’t believe that the European Union is doing either of those things and so I believe it is up to our Government to challenge them on that and the fact that they are separating out Northern Ireland from the rest of the United Kingdom.”
Mrs Foster said the issues with the protocol are “fundamental”, adding: “You can’t even get a pot plant from Great Britain into Northern Ireland at the moment which is absolutely incredible.”
She said she did not regret supporting Brexit but said it was “important that we deal with” issues with the protocol.
The European Commission’s vice president will meet with Mr Gove later over the Northern Ireland Protocol.
Maros Sefcovic is travelling to London for the meeting after making it clear the bloc regards the protocol as the only way forward.
Mrs Foster accused Mr Sefcovic of “putting his head in the sand” at a meeting over the protocol last week.
Mrs Foster told ITV’s Peston: “I wasn’t surprised because I sat in on the meeting between Michael Gove and Maros Sefcovic last week and it really was an occasion of putting his head in the sand and his fingers in his ears.
“There was complete as if nothing had happened the Friday before in terms of the Article 16 triggering by the European Commission and that we should just all move along and pretend that it hadn’t happened.
“But worse than that in his response actually to Michael Gove this evening he is actually asking for more protocols.
“So the answer to the difficulties with the protocol and the fact that we have this real problem for trade between Great Britain and Northern Ireland, in other words internally in the UK single market, is actually more protocol – we need to be tighter on the protocol – and I think that that is an incredible state of affairs.”
Asked what Mr Gove might be able to get from the EU, she said: “The EU need to understand in reality what the Belfast Agreement says.”
Mr Sefcovic has said the Northern Ireland Protocol is the “only way” to protect the Good Friday Agreement.
In a letter to Cabinet Office Minister Michael Gove on the eve of their meeting in London, he wrote: “The United Kingdom’s withdrawal from the Union, its single market and its customs union presents unique and significant challenges for the island of Ireland.
“The protocol is the solution agreed by the UK and the EU to these challenges: it is the only way to protect the Good Friday (Belfast) Agreement, preserving peace and stability and avoiding a hard border on the island of Ireland.
“It is designed to ensure clarity and predictability for people and businesses, while minimising the disruption inevitably caused by the withdrawal of the United Kingdom from the European Union. It is a balanced outcome after years of difficult negotiations and is now our mutually agreed legal obligation.
“I therefore agree that our shared objective is to work tirelessly in order to make the protocol work. It requires full and faithful implementation by both parties.
“The Union’s commitment to the objectives of the protocol on Ireland/Northern Ireland, as a cornerstone of both the Withdrawal Agreement and the relationship between the European Union and the United Kingdom, is unwavering.”
A UK Government spokesperson said it was “disappointing” that the Commission had “failed to acknowledge the shock and anger felt right across the community in Northern Ireland from its decision to trigger Article 16, and the need to take urgent steps to restore confidence as a result”.
“The Chancellor of the Duchy of Lancaster will underline the need for such action and political leadership in this regard when meeting with Vice-President Sefcovic in London tomorrow,” the spokesperson added.
UUP leader Steve Aiken said the letter “reeks of arrogance and intransigence”.
“Instead of protecting the Belfast Agreement and defusing tensions, this letter will do the exact opposite,” he said.
He also claimed that Northern Ireland is being used as a “punchbag in the EU`s confrontations with the UK Government”.
On Wednesday European Commission president Ursula von der Leyen apologised for “mistakes” that led to the triggering of Article 16.
However Mr Sefcovic has made it clear in his letter that the commission regards the protocol as the only way forward.
“The protocol is the solution agreed by the UK and the EU to these challenges: it is the only way to protect the Good Friday (Belfast) Agreement, preserving peace and stability and avoiding a hard border on the island of Ireland,” he wrote.
“It is designed to ensure clarity and predictability for people and businesses, while minimising the disruption inevitably caused by the withdrawal of the United Kingdom from the European Union.
“It is a balanced outcome after years of difficult negotiations and is now our mutually agreed legal obligation.
“I therefore agree that our shared objective is to work tirelessly in order to make the protocol work.
“It requires full and faithful implementation by both parties.”
