In an unusually strong language against a member nation, the EU Justice commissioner Viviane Reding deplored France's deportation of more than 1,000 Roma to Romania and Bulgaria since August as a "disgrace" for the 27-nation group.
Reding said she is appalled that the deportation of the Roma is reminiscent of the situation in Europe during the World War II when thousands of Jews and Sintis (Roma) were deported by the Nazi Germany.
"I personally have been appalled by a situation which gave the impression that people are being removed from a member state of the European Union just because they belong to a certain ethnic minority," Reding said during a news conference in Brussels.
"This is a situation I had thought Europe would not have to witness again after the Second World War."
The French government has been defending the deportations arguing that the authorities are closing down "illegal" Roma camps, which it associates with crimes, prostitution and child abuse.
The government also claims that most of the deportees are leaving voluntarily, taking advantage of cash payment of about 330 euros per adult and 100 euros per child.
Discrimination on the basis of ethnic origin or race has no place in Europe, Reding said, adding that it is incompatible with the values on which the European Union is founded.
National authorities who discriminate ethnic groups in the application of EU law are also violating the EU charter of fundamental rights, which all member states, including France have signed.
"I therefore find it deeply disturbing that a member state calls so gravely into question, by the actions of its administration, the common values and the law of our European Union," she said.
The commissioner also rebuked the French authorities for contradicting recent assurances given to her by two cabinet ministers that Roma minorities have not been specifically targeted for deportation.
She referred to a circular from the French interior ministry to regional police authorities demanding that 300 Roma camps or illegal settlements must be cleared within three months.
The circular, which was published by the French press on Monday, said "three hundred camps or illegal settlements must be cleared within three months, Roma camps are a priority."
She also pointed out that the French interior minister signed a new circular yesterday afternoon "eliminating the references to a particular ethnic group, the Roma."
Reding said she is convinced that the commission will have no choice but to take infringement action against France and a decision is expected within two weeks.
Then the case will be taken to the European court of Justice in Luxembourg.
The European Commission's preliminary analysis of the French expulsion showed that France would be in violation of the EU law if the measures taken by the French authorities in applying the Free Movement Directive had targeted a certain group on the basis of nationality, race or ethnic origin.
She also took issue with the statement by the French Minister for European Affairs Pierre Lellouche yesterday questioning the role of the European Commission as the guardian of the EU treaties.
"The commission’s role as the guardian of the treaties is one of the foundations of the European Union – a union which is held together not by force, but by respect for the rule of law agreed upon by all member states, including France," she said.
The European commission's warning to France comes a week after the European Parliament in Strasbourg sharply condemned France’s treatment of Roma minorities and demanded an immediate end to their deportations.
In a strongly-worded resolution passed by the parliament, 337 MEPs also demanded the European Commission and EU governments to take urgent steps to protect the Roma minorities from exploitation and to integrate them into the society.