A leaked letter from the North's top official shows Theresa May's Government was warned about significant problems with its Brexit plans last August.
David Sterling, the head of the civil service in the North, told senior UK Brexit official Olly Robbins the plans for a customs partnership with the EU - seen as a way of avoiding a hard border with the Republic of Ireland - presented a "significant challenge".
In a letter written in August 2017, just days after the Brexit department published position papers on the future customs arrangements and the North and Ireland, Mr Sterling highlighted a series of issues which needed further work.
The "customs partnership" set out as one of the options by the Government would involve the UK effectively applying Brussels' rules and tariffs after Brexit on goods arriving in the country but destined for the EU market.
Under the heading "back door risk", Mr Sterling said the "visibility and impact" of the "robust enforcement mechanism" necessary to enforce the plan presented a "significant challenge".
Even if the customs plan worked, other difficulties remained in maintaining cross-border trade, he added.
"The example of Turkey illustrates that customs duties are only one part of the picture and technical barriers can be equally disruptive to trade.
"Potential trade barriers created by diverging tariffs or regulatory standards are therefore a key area for ongoing discussion."
He also cast doubt on the proposal for an exemption for small traders crossing the border between Northern Ireland and the Republic.
"The dividing line between businesses of different sizes in Northern Ireland supply chains will undoubtedly be blurred," he said.
That could make it "difficult" to define which firms were exempt.
The document was one of a series of leaked papers disclosed by the GUE/NGL group in the European Parliament, which includes Sinn Fein.
At the time the letter was sent, Mr Robbins was the senior civil servant at the Department for Exiting the European Union and he now serves as the Prime Minister's Europe adviser and co-ordinator of the Brexit negotiations with Brussels.
The Department for Exiting the European Union said it would not comment on leaked documents.
Green co-leader Caroline Lucas, a supporter of the Best for Britain campaign, said: "It's shocking that just months away from a potential leave date we're seeing top officials liken the potential situation in Northern Ireland to that of Turkey.
"There is a hard border between Turkey and the EU, and the implementation of such a border between Northern Ireland and Ireland would be a huge blow to the hard won peace in the region."