The European Commission said Hungary and Poland have accepted no asylum seekers, and the Czech Republic has accepted 12 of the 2,000 it was required to take.
The move was an attempt to relieve pressure on Greece and Italy where the vast majority of migrants were arriving.
While most of the member states had relocated the migrants, the Czech Republic, Hungary and Poland had failed to apply the measures fully.
The commission launched infringement procedures against the three states in June and warned them last month that further action was likely.
The EU took Hungary to the bloc's top court on Thursday over a crackdown on education and foreign-backed civil society groups that critics say targets USA billionaire George Soros.
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But, "the replies received were again found not satisfactory and the three countries have given no indication that they will contribute to the implementation of the relocation decision", the Commission said in a statement.
Andrej Babis told the local CTK news agency on Thursday, a day after he was sworn in as prime minister, the system to relocate the refugees is "nonsense" that only supports the popularity of extremist parties in Europe.
The temporary emergency relocation scheme was established in two Council Decisions in September 2015, in which Member States committed to relocate persons in need of global protection from Italy and Greece. The Commission also took legal proceedings over Hungary's asylum law to the next step, by issuing a formal request for Budapest to comply with European Union law.
Hungary's right-wing government is looking to pass a higher education law that could close the Central European University, founded by financier and philanthropist George Soros.
Hungary has been given a deadline of two months to respond to the latest step in the Commission's action over the law.