The government’s medicines watchdog has warned that leaving the EU could jeopardise its ability to protect public health.

The annual accounts of the Medicines and Healthcare Products Regulatory Agency (MHRA) outline several possible dangers.

One is that Brexit threatens to “impact on the ability of the agency to undertake its public health protection role”. Another is that the agency fails to fulfil its statutory duties because it loses funding.

According to the Commons Library, the European Medicines Agency (EMA), which will quit London after Brexit, outsources up to a third of its work to the MHRA and provides a third of its income.

Experts fear patients will have to wait up to two years longer for new drugs after Brexit, because drug companies would approach the EMA, which evaluates drugs in the EU, for approval before coming to the MHRA.

Leslie Galloway, chairman of the Ethical Medicines Industry Group, which represents the UK pharmaceutical industry, said: “The MHRA’s warnings about Brexit should be taken very seriously. Without clarity on how the UK will work with the EU post-Brexit, there is a real risk that patients will have to wait up to two years longer for medicines, and pharmaceutical companies will disinvest in the UK. That would be bad for patients [and] bad for the NHS.”

The MHRA said its accounts acknowledged the risks embedded in EU processes “if we do not get implementation of a successor regime right”.

The Department of Health said: “We continue to play a full role in the EU medicines regulatory framework, and we will work closely with our European counterparts to ensure continued cooperation, in the best interests of business, citizens and patients across the EU and the UK.”