Labour and the Democratic Unionist party have formed an unprecedented alliance to demand that the government explains whether Northern Ireland’s fishing waters will be controlled from London if Boris Johnson’s proposed Brexit deal becomes law.

In a sign of further confusion over how prime minister’s withdrawal agreement will work, the parties’ fisheries spokesmen have written to the environment secretary, Theresa Villiers, asking why her department appears to claim that fish caught in waters off the coast of Northern Ireland will no longer be classed as Northern Irish fish.

Labour’s Luke Pollard and the DUP’s Jim Shannon wrote that the province’s fishing industry of 300 boats were questioning who will be in charge over customs, taxes, visas and enforcement of rules.

The letter, sent before parliament dissolved for the election and leaked to the Guardian, can be disclosed after Johnson appeared to misunderstand his own Brexit deal on a visit to Northern Ireland on Thursday.

In a video shot in Northern Ireland on Thursday night, Johnson told exporters they would not need to fill in customs declarations when they sent goods across the Irish Sea, adding that if firms were asked to they should call him and he would “direct them to throw that form in the bin”.

This contradicted the view of Stephen Barclay, the Brexit secretary, who told a House of Lords committee that businesses would need to complete “exit summary declarations” for such sending shipments.

In the letter, Pollard and Shannon wrote: “We are taking the unprecedented step of writing a joint letter to you as the Labour and the DUP’s spokespeople on fisheries to raise concern about the Brexit deal and fisheries in Northern Ireland.”

In the final week of October, officials from the Department for Environment, Food and Rural Affairs (Defra) told the Northern Irish fishing industry that direct landings of fish into Northern Ireland would be subject to new obligations as if they were landing in an EU port, they wrote.

“This would include the requirement to issue catch certificates and they [the officials] warned that tariffs could apply to these landings,” the letter said.

The letter points out that the department’s press office attempted to clarify matters by issuing a second statement to the Guardian, which said: “The Northern Ireland protocol in the withdrawal agreement bill applies EU customs legislation in Northern Ireland but excludes the territorial sea.”

The letter continued: “This seems to suggest that Northern Ireland’s territorial waters are excluded from the Northern Ireland protocol, meaning they remain in the GB customs and VAT territory and not in the Northern Ireland/EU customs territory.

“These two statements seem to suggest that the fish caught by Northern Irish fishers off the coast of Northern Ireland may no longer be classed as Northern Irish fish. This would suggest that the border the prime minister promised he would not introduce, but has, is not in the middle of the Irish sea but on the quaysides and beaches of Northern Ireland,” they wrote.

The letter posed a series of questions about regulation and taxes. It added: “If a Northern Irish vessel departs a Northern Irish port and catches fish in what was, until now, Northern Irish waters and returns to the Northern Irish port with their catch, will tariffs, prior notification, catch certificates and additional paperwork be required?”

The government has not replied to the letter, according to Labour sources.

Asked for a response by the Guardian, a government spokesman said: “We have renegotiated a new deal which allows us to leave the EU without disruption. Tariffs will not apply to Northern Ireland exports to the EU, including exports of fish landed by Northern Ireland fishing vessels.”