France had right to halt migrant trains from Italy - EU
Home Affairs Commissioner Cecilia Malmstroem said French officials had cited "public order reasons".
An EU spokesman also said France was not obliged to grant entry to people with the temporary residency permits given to some migrants by Italy.
Italy complained that the move violated EU rules on the free right to travel.
For those legally living in the 25 countries in the Schengen Area - to which France and Italy belong - no travel documents are required.
’Strong protest’
Earlier on Monday, the French interior ministry said the rail link between Menton, France and Ventimiglia, Italy, was operating normally.
It said there had been an "isolated problem" caused by hundreds of activists on one train planning an "undeclared demonstration" in France, and posing a problem to public order that was temporary in nature.
"At no time was there a... closing of the border between France and Italy," spokesman Pierre-Henri Brandet said.
He estimated that up to 10 trains may have been affected by the disruption, five on each side of the France-Italy border.
The statement came after the Italian ambassador in Paris was instructed by Foreign Minister Franco Frattini to lodge a "strong protest" of the blocking of the trains. The ambassador called the move "illegitimate and in clear violation of general European principles".
While Mr Frattini acknowledged that the activists might have given them a cause of concern, he insisted it was not a "sufficient reason to justify sealing one of the most heavily used and sensitive European borders".
The migrants had the proper paperwork to enter France, he added.
Italy has been giving temporary residence permits to many of the 26,000 Tunisians who have entered the country illegally to escape the unrest in the region in recent weeks, overwhelming refugee centres. Many have ties to France, and Italy says they should be able to travel there.
France has said it will grant entry to migrants holding the permits only if they can demonstrate that they can support themselves financially.
At a news conference on Monday afternoon, Ms Malmstroem said she had received a letter from France explaining the "temporary" disruption was the result of "public order reasons".
"It may be that this is not covered by the Schengen border code rules. But it would seem that they had the right to do this," she said.
EU spokesman Michele Cercone also said the residence permits were not visas, and France was under no obligation to admit people having neither EU visas nor EU passports.
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