The protocol has resulted in significant unresolved problems with the supply of medicines to Northern Ireland, according to a House of Lords Committee.
NI is still covered by the pharmaceutical regulatory framework of the European Union thanks to the post-Brexit agreement, also known as the protocol.
The EU acknowledged that this was leading to real issues and amended some of its laws to address the issue.
However, the Lords claim that additional measures will be required to prevent supply disruption.
"There is a general assumption that the EU legislation that took effect in April 2022 has resolved the issues with the supply of medicines to Northern Ireland," said Lord Jay of Ewelme, chair of the subcommittee on the Northern Ireland Protocol.
"This is obviously false. The legislation was beneficial insofar as it went, but it is obvious that important problems remain unresolved.
"While the outcome of the UK-EU negotiations over the protocol's future is awaited, the provision of medicines to Northern Ireland must not be neglected under the mistaken belief that the issues have been resolved. '.
The operation of the protocol has been the subject of intense negotiations between the UK and the EU, and the prime minister was supposed to announce a deal this week.
However, the Democratic Unionist Party (DUP) and some Conservative MPs are opposed to his plans because they believe they won't go far enough.
It's unclear at this time whether any new agreement will modify the laws governing medications further.
The committee was informed that the application of the EU Falsified Medicines Directive (FMD) to Northern Ireland but not to Great Britain is "the single biggest factor" causing ongoing difficulties.
It imposes requirements on distributors shipping goods to Northern Ireland, such as sample verifications of all medicine packs and product inspections and decommissioning before being delivered to any healthcare facility in Northern Ireland that is not a hospital, pharmacy, or doctor's office.
The additional administrative burden of turning off security features as a product enters Great Britain and turning them back on as it enters Northern Ireland applies to medicines traveling from the EU to Northern Ireland via Great Britain.
However, the committee claimed that the issue that these procedures are meant to address is "minuscule," as there have been no reports of serious problems with fake medication in Northern Ireland.
The UK government is requiring a change to the licensing of some medicines, which is the other significant issue.
In practice, some products that are currently sold under an EU license will need to switch to a GB license, resulting in a difference in the licensing standards between GB and NI.
Some manufacturers have cautioned that the production of Northern Ireland-only packs, which will be necessary as a result of this change, would not be commercially viable.
The committee was informed that the UK government had the power to stop the regulatory change that would cause the divergence.
It has written to the government to inquire about the steps it is taking to find a long-term solution to the licensing problem before the end of 2023, in cooperation with the EU.
The committee also emphasized that, in addition to the protocol, there were other factors that affected medicine supplies.
"Our witnesses pointed out that the issues with the supply of medicines to Northern Ireland are part of a larger set of problems affecting the industry, including the wider impact of Brexit on supply chains and product testing, problems with global supply chains, and shortages and rising prices of goods since the COVID pandemic," the statement read.
"As a result, it is challenging to distinguish between the impact of the protocol and other factors.
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