Trains were stopped at the France-Italy border for hours, the BBC has reported. Services were later resumed.
A spokesman for Italy's rail company told the BBC that trains were not allowed to pass into Menton, France, from the Italian border station of Ventimiglia.
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The incident has prompted Italy to launch an official complaint with France.
The Italian foreign ministry described France's actions as "illegitimate and in clear violation of general European principles".
Italy has given temporary resident permits to thousands of Tunisian migrants, which allow them to travel freely in many European countries.
