Concerns over reports of plans for a new sea route between Ireland and the EU mainland are shared by Welsh Secretary Alun Cairns, Wales Office minister Guto Bebb has told MPs.
Labour MP Albert Owen said a company has proposed a new route between Ireland and Holland and Belgium.
Mr Bebb said the UK government wanted a "frictionless border" at Holyhead.
Brexit secretary David Davis has warned of potential complexity at the port post-Brexit.
The UK government has committed itself to avoiding a hard border in Ireland, although the Irish government has asked for more detail.
"Last week a company from Ireland suggested a new route to Holland and to Belgium, circumnavigating Britain," Mr Owen told the Commons.
"Stakeholders in my constituency are concerned about this. The Irish government is concerned about this, so is the Welsh Government."
Mr Bebb said: "The honourable gentleman raises an important point about the port of Holyhead, and the concern is shared by my right honourable friend the secretary of state for Wales"
"I can assure the honourable gentleman that our intention is to ensure a frictionless border in Holyhead, in the same way as in Ireland."
Earlier, Mr Bebb was questioned about the future of economic aid to poorer parts of Wales after Brexit, telling the Commons billions of pounds of EU money had been "wasted" by the Welsh Government.
He said EU structural funds designed for the poorest parts of the EU had been a "failure" in Wales.
The UK government plans to replace EU funding with a UK-wide "shared prosperity fund" after Brexit.
Shadow Wales Office Minister Chris Ruane complained there was a lack of clarity about the future of the funds and asked for the funding to be maintained after Britain leaves the EU.
Mr Bebb told him: "You raise a question about EU structural funds as if they were a success in a Welsh contest. They were actually a failure in a Welsh context. £4bn of investment and yet our comparative economic performance fell."