The European Commission's decision comes after the three countries decided not to take in refugees under a 2015 plan.
The European Union launched legal action on Tuesday against three Eastern European countries for refusing to take in their share of refugees under a controversial solidarity plan.
"I regret to say that despite our repeated calls, the Czech Republic, Hungary and Poland have not yet taken the necessary action," EU migration Commissioner Dimitris Avramopoulos told a press conference.
"For this reason, the [European] Commission has decided to launch infringement procedures against these three member-states."
Hungary's parliament on Tuesday approved strict new rules for non-government organisations with foreign funding in a further escalation of the government's conflict with Hungarian-American billionaire George Soros.
Defying calls from the European Parliament and human rights groups to drop the bill, it passed a law drafted by right-wing populist Prime Minister Viktor Orban's government that requires NGOs that get money from abroad to register with the authorities.
The government says it wants to ensure greater transparency and protect Hungary from foreign influence, but NGOs and human rights groups say the bill stigmatises them and is intended to stifle independent voices in the central European country.