In order to settle disputes concerning the implementation of the Protocol on Ireland/Northern Ireland, the UK-EU Withdrawal Agreement provides for two types of dispute-settlement mechanism. 

For matters concerning the implementation of applicable EU law, standard EU procedures apply. According to Article 12(4) of the Protocol, 'the institutions, bodies, offices, and agencies of the Union shall in relation to the United Kingdom and natural and legal persons residing or established in the territory of the United Kingdom have the powers conferred upon them by Union law.' This means, for example, the UK acts can be challenged directly before the Court of Justice of the EU. It also means that individuals can invoke their rights and obligations under the Protocol before UK courts and questions relating to the interpretation or validity of EU law may be referred to the Court of Justice of the EU.

For other matters concerning the implementation of the Protocol there is a dispute-settlement procedure provided for in Articles 167-181 of the Withdrawal Agreement. This can lead to matters being referred to an Arbitration Panel. 

Finally, beyond the Protocol, both EU and the UK acts can be challenged in accordance with the judicial review mechanisms established in their respective legal systems.  

EU concerns during 2020-2021 over the extent to which the UK was fulfilling its obligations arising out of the Withdrawal Agreement and the Protocol in particular saw the European Commission notifying the UK government that it was either launching or was considering launching proceedings under both dispute-settlement mechanisms.  

UK Courts have also been presented with cases relating to the Protocol. These concern applications for judicial review of UK government actions relating to the Protocol's adoption and implementation.

Given the unique customs and trade arrangements established by the Protocol for Northern Ireland - formally part of the UK customs territory, but de facto part of the EU customs territory - concerns have been raised that the arrangements, or at least aspects of them, could lead to disputes with members of the World Trade Organization.