Lord Frost, who was the prime minister’s chief Brexit negotiator, also warned that solutions must be found rapidly.
Following his first official visit to the region he urged the EU to take a "pragmatic approach" to Northern Ireland protocol.
Effectively creating a border down the Irish Sea, it is hated by Unionists and has been blamed by some politicians for disrupting Northern Ireland’s fragile peace process.
It is not the first time the UK and the EU have been at loggerheads over the protocol.
Last month the secretary of state for Northern Ireland Brandon Lewis attempted to put pressure on the EU over the agreement, calling on it to "fully understand" the importance of identity to Northern Ireland’s loyalists.
And in March Brussels threatened legal action after Conservative ministers announced plans to unilaterally extend a ‘grace period’ designed to allow UK supermarkets and suppliers time to adapt to new trade barriers across the sea.
Maros Sefcovic, vice president of the European Commission, said that would be a “violation” of the protocol the UK agreed to.
After his trip, Lord Frost said: “It’s clear from my visit that the protocol is presenting significant challenges for many in Northern Ireland.”
"Businesses have gone to extraordinary efforts to make the current requirements work, but it is hard to see that the way the protocol is currently operating can be sustainable for long. " He added: “We’re committed to working through the issues with the EU urgently and in good faith. I hope they will take a common sense, risk-based approach that enables us to agree a pragmatic way forward that substantially eases the burdens on Northern Ireland.”
"Solutions must be found rapidly in order to protect the Belfast (Good Friday) Agreement in all its dimensions and to minimise disruption to the everyday lives of people in Northern Ireland - as the protocol itself requires. As the Prime Minister has made clear, we will continue to consider all our options in meeting our overriding responsibility for sustaining the peace and prosperity of everyone in Northern Ireland.”
Lord Frost met with business representatives from sectors including aerospace, manufacturing, food and drink, retail and life sciences while on a two-day visit to Northern Ireland.
He also visited the port of Larne to see how new checks and controls under the protocol are being operated.
He is understood to have heard concerns about the level and complexity of paperwork required even on goods remaining in Northern Ireland, as well as about disruption to supply chains from Great Britain.
Mr Lewis said: "It is vital that the experiences, opportunities and challenges faced by people and Northern Ireland are understood and at the heart of our approach. I will continue these constructive and practical discussions in the weeks ahead, supporting Northern Ireland’s business needs and minimising the risk of disruptions at a crucial time."