“EU values and fundamental rights must be respected by Member States and state authorities,” European Commissioner for Equality, Helena Dalli, wrote on Twitter.
“This is why six town-twinning applications involving Polish authorities that adopted ‘LGBTI free zones’ or ‘family rights’ resolutions were rejected,” she added.
Under the terms of the program — which provides funding of up to €25,000 ($29,000) — the scheme should be accessible to all European citizens, without any form of discrimination.
Commission spokesman Adalbert Jahnz said: “Six applications have been rejected because the answer given by the legal representative of the project did not provide the evaluation committee with sufficient assurance that the project would be in line with those objectives and general features.”
Jahnz told CNN he was “not at liberty” to identify the rejected applications, adding: “We do not disclose the applicants who were rejected to get EU funds, this is a really a principle of equality of treatment that is at the heart of our selection processes.”
In a statement on Twitter, European Commission President Ursula von der Leyen said: “Our treaties in Europe ensure that every person in Europe is free to be who they are, live where they like, love who they want and aim as high as they want. I will continue to push for a #UnionOfEquality.”
While Polish attitudes toward homosexuality are slowly progressing, same-sex marriage is not legal and the overwhelmingly Catholic country remains one of the most conservative and restrictive in Europe for LGBTQ people.
Earlier this month a city in the Netherlands severed ties with its sister city in Poland after the latter declared itself an “LGBT-free zone.”
Nieuwegein, a city near Utrecht in central Netherlands, released a statement announcing the immediate end to its friendly relationship with the Polish city of Pulawy.
The Nieuwegein City Council called on the municipal executive council to sever ties on July 13 after becoming aware of recent reports on the treatment of members of the LGBT community in Pulawy.
CNN has attempted to contact local authorities in Pulawy for comment.
Jack Guy and Martin Goillandeau contributed to this report.