The British government has rejected an EU request to open an office in Belfast, in the first major row over the implementation of the post-Brexit Irish border protocol.

The EU closed its offices across the UK when the country left the bloc on 31 January, but its officials have a right to be present to monitor the checks and controls on goods crossing the Irish Sea.

The Foreign Office has rejected Brussels’ request for a permanent physical presence in Belfast on the grounds this would go beyond what is stipulated in the withdrawal agreement.

There are concerns it would be seen by some as a step towards joint policing of the customs border between Northern Ireland and the rest of the UK.

The British government fought during negotiations over the withdrawal agreement to ensure that checks and controls on goods crossing the Irish Sea would not be jointly carried out.

The row highlights the potential for the protocol on Northern Ireland to be a cause of contention between the EU and UK in the months to come.

Under the withdrawal agreement, Northern Ireland effectively stays in the single market. It also remains within the UK’s customs territory to allow it to benefit from any future trade deals secured by the British government. But the full EU customs code has to be enforced on goods travelling between Northern Ireland and the rest of the UK. All goods deemed at risk of travelling from Northern Ireland into the Republic of Ireland would attract tariffs.

The messy compromise allowed for the avoidance of a border on the island of Ireland but brings with it a host of potential flash points.

The issue of a Belfast office was raised on Monday during the first teleconference meeting of the EU-UK joint committee, set up to supervise the operation of the withdrawal agreement. The chancellor of the Duchy of Lancaster, Michael Gove, is the UK’s senior figure on the committee.

Under article 12 of the Northern Ireland protocol, the UK government is “responsible for implementing and applying the provisions of [EU] law” but EU officials “shall have the right to be present during any activities” relating to checks and controls.

The UK is obliged to “facilitate such presence of representatives and shall provide them with the information requested”. The EU wants a base for its customs and veterinary experts.

A European commission spokesman said: “We can confirm that we have sent letters to the UK regarding a proposal to open a technical office in Belfast with specific technical capabilities to ensure the implementation of the protocol on Ireland/Northern Ireland. This issue was raised in the joint committee on Monday. We remain in contact with the UK on this point.”

A cross-party group of members of the Northern Ireland assembly has written to the prime minister backing the commission’s proposal.

Michelle O’Neill of Sinn Féin, who is the deputy first minister of Northern Ireland, along with the leaders of the Greens, the Social Democratic and Labour party and the Northern Ireland Alliance, wrote: “As party leaders representing a majority of citizens who voted to remain within the EU, we feel strongly that an office in Belfast is necessary to ensure the implementation of the protocol on Ireland/Northern Ireland which you negotiated with the EU …

“To oppose the opening of such an office by the EU in Belfast represents an act of bad faith by your government and a breach of trust at this critical stage of the process.”

A spokesman for the UK government said it was considering the issue. He said: “We received an initial request from the EU and responded to decline the proposal in February. We have since received a follow-up letter to which we will respond in due course.”