The former Taoiseach said the contentious post-Brexit arrangements are not properly understood by the community, and viewed as a backdoor to a united Ireland.
He said: “I spend a lot of my life still in the North. The reality is in East Belfast and in the ghettos and in the areas where you’re likely to get trouble, is that people haven’t got a clue about the protocol, not a clue.
“They see it as identity.
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“They see it as a road to the Dublin Government taking over again and this is a pathway to that. That’s the hard reality.”
The protocol was designed to prevent a hard border on the island of Ireland, by introducing controls in the Irish Sea on goods travelling between Britain and Northern Ireland.
The EU and the UK remain deadlocked in negotiations over its implementation, with the new barriers to east/west trade creating tensions in some loyalist and unionist communities.
Mr Ahern, a former Fianna Fail leader and one of the architects of the Good Friday Agreement, said the idea that Protocol is about trade “just passes them by”.
He added: “In fact they’re not interested. It’s seen as a trick by the south to move the border from across the island, and to put it down the Irish Sea, as a trap for government.
“That’s how they see it. Even those who you might consider to be a bit more intelligent and articulate. That is the difficulty.”
Mr Ahern said negotiations over the protocol are made more difficult by this view.
He said: “We’re trying to do two things. We’re trying to solve the difficulties of medicine and meats and everything else in the protocol.
“But there’s another issue in the protocol, and that’s what is in the head and the ideological one, and that’s a far more difficult one to deal with.
“(DUP leader) Jeffrey Donaldson well understands how we might get over the detail, and the reason he keeps on about the other issue is because he’s trying to – which I don’t blame him for – he’s trying to serve the loyalist community as well.”
Speaking earlier, Irish Foreign Minister Simon Coveney said the EU had offered a comprehensive package to the UK, aimed at easing the implication of the Protocol.
He said: “This package represented a significant compromise for the EU.
“The lack of any evident reciprocal willingness to compromise from our UK partners to date has been deeply disappointing.
“The protocol was agreed by Lord Frost and Prime Minister Johnson, approved by this British government and ratified by the current UK Parliament.
“They have a duty to deliver on their commitments.
“It is very important we do not lose sight of the goal here, ensuring an outcome that is best for the people of Northern Ireland.”