The European Medicines Agency has revealed a list of five cities that are preferred as its new location by staff after Brexit, following warnings of a public health disaster if EU leaders pick the wrong location later this year.

Amsterdam, Barcelona, Copenhagen, Milan, or Vienna came top of the staff survey, while the agency warned that it could lose more than 70% of its staff if politicians decide to relocate to Athens, Bratislava, Bucharest, Helskinki, Malta, Sofia, Warsaw or Zagreb in a vote in November.

However the survey was conducted before the recent referendum and violent protests in Barcelona, which led to Catalonia threatening to secede from Spain and potentially the European Union.

The agency had previously published the findings of its staff survey but without naming the preferred and least preferred cities, with dire warnings about staff retention and outcomes for drugs regulation should politicians choose the wrong location in a complicated voting system.

The agency published the documents containing the preferred cities after its executive director, Guido Rasi warned in an interview that access to new drugs and safety monitoring of approved medicines could be jeopardised if the politicians pick the wrong location for the EMA’s new HQ.

The European Commission over the weekend published its assessment of the bidding cities, but did not rank them.

Rasi told Reuters: “Oncology is a good example. The pipelines are very promising for new cancer options and if there is severe disruption those might be delayed or prove impossible to approve.”

The agency has been based in London since it started operations in 1995 and has a staff of around 890 people.

Relocating the EMA before March 2019 will therefore be tough, as was demonstrated by the three-year period it took to move it to a new office block close to its original home in Canary Wharf in 2014.

Rasi said that he would stay on in charge wherever the agency moves. “The captain is the last to abandon the ship,” he said.

In a separate development, a European court ruled on appeal that there was no irregularity with the recruitment procedure and appointment of professor Guido Rasi as the European Medicines Agency’s executive director in 2011.

Rasi had to step down from the role in 2014 after a candidate appealed against the decision by the European Commission not to include him on the shortlist for the job.

This was because the European Union Civil Service Tribunal annulled the European Commission’s shortlist of potential candidates in November 2014, and in effect over-ruled the EMA management board’s selection of Rasi from the shortlist.

The EMA therefore had no executive director between November 2014 and November 2015, with deputy director Andreas Pott stepping in to represent the agency during this period.

Rasi took an advisory role during this period, then re-applied for the position and was reappointed in October 2015.