The European Medicines Agency, one of the biggest EU regulators and one of the first casualties of Brexit, has closed its doors in the UK for the last time with the loss of 900 jobs.

Staff lowered and folded up the 28 national flags that adorned the lobby in the company’s Canary Wharf headquarters in London on Friday night, bidding it farewell before moving to their new offices in Amsterdam.

The EMA evaluates medicines throughout the EU but was forced to relocate to the Dutch capital because pharmaceuticals regulation should be done in a member state. Amsterdam won the bid to host the agency in 2017.

Its departure from London was lamented widely as it marks not just the loss of highly skilled jobs but the UK’s central place in pharmaceutical evaluation and monitoring.

In a tweet on Friday evening, the agency said: “Today, EMA staff lowered the 28 EU flags and symbolically said goodbye to their London offices. [EMA executive director,] Guido Rasi expressed his thanks to the UK for its contribution to the work of the Agency and for having been a gracious host of EMA since 1995.”

Jeremy Farrar, the director of the Wellcome Trust, said it was a “very sad day for the UK” and “a great day for the Netherlands”.

The Labour MEP Claude Moraes said also expressed disappointment about the move, writing on Twitter that he was “obv[iously] sad that you to have to leave London.”

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Simon Fraser, the vice chair of Chatham House and the former permanent secretary at the Foreign Office, wrote: “Losing the European Medicines Agency HQ is a significant loss for London and for the UK.”

The decision made by the EU to move the EMA was a body blow to those who have spent a lifetime charting the progress of medicines through evaluation and testing cycles.

In September it emerged that Britain’s leading role in evaluating new medicines for sale to patients across the EU had collapsed with no more work coming from Europe because of Brexit.

The head of the Association of British Pharmaceutical Industry, Mike Thompson, said at the time it was akin to watching a “British success story” being broken up.