Both the European Medicines Agency (EMA) and the European Banking Authority (EBA) are currently based in London with EU bosses keen for a quick move for the lucrative organisations.
The EMA and EBA attract thousands of visitors each year providing a boost for hotels and restaurants in the host city.
Up to 21 capital cities are said to be lining up to host the agencies, which have been dubbed the crown jewels of the EU.
The EU is ready to vote on the new location for two major agencies
Member state governments will have until July 31 to submit their bids with a final decision to be made by October
The agencies employ more than 1,000 people with the EMA alone attracting 36,000 visitors including scientists and health professionals in 2015.
Member state governments will have until July 31 to submit their bids with a final decision to be made by October according to guidelines set out by European Commission President Jean-Claude Juncker and European Council President Donald Tusk.
Voting will take place on the margins of a meeting of European affairs ministers in October, according the 18-page May 19 paper.
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France has the highest score in the index at 32.5
Mr Juncker and Mr Tusk stressed "the business continuity of the two agencies is vital and must be ensured".
The European Commission will review the national offers with the new host city expected to be ready to host the agencies by the day Britain leaves the EU in 2019.
Guidelines seen by the Wall Street Journal say the European Commission will assess bids on a series of strict criteria including airport access and local schools.
Countries can bid for both agencies but will only be allowed to host one with the EMA, which decides if medicines are safe for the European Single Market, said to be the top prize.
Leading contenders to house the EMA are already jockeying for position, with Spanish Health Minister Dolors Montserrat setting out the case for Barcelona to host the agency during a visit to Brussels on Wednesday.
She said: “Barcelona is ready to host the EMA now. No-one is offering a better combination of location, facilities, services and a high quality of life from both a professional and social perspective than Barcelona."
European Commission President Jean-Claude Juncker set out the guidelines
European Council chief Donald Tusk also sent out the guidelines
Milan, Copenhagen and Dublin are also said to be putting in offers for the EMA which employs nearly 900 highly-skilled staff and has an annual £277million budget.
Vying member states must be able to compete with real estate on a par with the current EMA and EBA headquarters.
The financial watchdog is currently based at Canary Wharf occupying 2,345 square metres of office space on the 40th floor of a skyscraper.
The EBA is currently based at Canary Wharf
France and Germany are competing for the EBA, which employs 160 staff, with Paris and Frankfurt vying to snatch the agencies from London.
But threats from France to block Frankfurt’s bid have seen EU bosses look to Brussels and Vienna as the next best options.
The move will leave a regulatory vacuum for UK business and industry with officials saying relations between regulatory bodies after Britain leaves the EU is a matter for Brexit negotiations in the run-up to the divorce scheduled for March 2019.