The government has come under increased fire as the three-year anniversary of the 13 November, 2007 ruling by the European Court of Human Rights approaches. The Council of Europe, a pan-European human rights watchdog, is set to review progress on 30 November.
The Czech Republic has failed Roma children, the human rights groups said in a statement.
Roma children in the Czech Republic "have continued to be shunted into substandard schools and classes for the mentally disabled," said James Goldston, executive director of the Open Society Justice Initiative, which was joined in the complaint by the European Roma Rights Centre and the Greek Helsinki Monitor.
EU officials should demand a stop to the segregation of Roma children and within six months adopt financial and legal measures to help them, he said.
Failure to comply with the court ruling could lead to a new court case and possible fines or sanctions.
Education minister Josef Dobes argued that amendments to legislation that would ban educating healthy children under the same conditions as the mentally disabled would be submitted to the government by t January 2011. It was not clear when they would become effective.
The legislation should "ensure equal access to education in our schools and I fully agree with it," he said. According to Amnesty International, Gypsies, or Roma, make up 80 per cent of the students in Czech schools for those with mild mental disabilities.