Italy has summoned the French ambassador after French border patrol agents used an Italian train station facility to have a Nigerian train passenger provide a urine sample for a drug test.

France said it had a right to intervene.

The humanitarian group Rainbow4Africa, which helps migrants at the Bardonecchia train station west of Turin, denounced what it called a "raid" on Friday night in their station workspace and accused the five armed French border agents of intimidating its doctor, cultural mediators and lawyers working there.

But French authorities said their border agents had the right to use the Italian facility according to a 1990 agreement.

In a statement, the French budget ministry, which is responsible for the railway agents, said they asked to use the facility to better respect the rights of the Nigerian, whom they suspected aboard the train of having drugs on him.

A volunteer who witnessed the incident told Sky TG24 that the Nigerian had Italian identity papers and a valid Paris-Naples train ticket.

The urine test turned out negative, the French statement added. The French said they were more than willing to explain the details to Italian authorities.

An Italian foreign ministry official, speaking on condition of anonymity because the consultations were ongoing, confirmed the French ambassador had been summoned.

Italian officials were outraged at the incident, with Bardonecchia Mayor Francesco Avato saying the French had no right to enter the facility, which he said the city operates with Rainbow4Africa as a "neutral" space to try to persuade migrants not to make the dangerous Alpine crossing into France.

Former Premier Enrico Letta denounced the "raid" as the latest error committed by one of Italy's partners in Europe's migration crisis.