Sea Eye and two other aid groups are halting migrant rescues in the Mediterranean after Libyan hostility.
The NGO said its ship was 44.5 km off Libyan coast when the Libyan coastguards had seized it.
A Reuters photographer, who was on board, claiemd the Libyan coastguard sent a message, in English, to the Golfo Azzurro's crew, accusing them of intruding in Libyan waters for several months and of "causing problems" to Libya.
Instead, the Azzurro headed away from Libyan shores.
The group released a picture of the Libyan vessel as well as an image of the coordinates of their ship.
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A Libyan coastguard spokesman in Tripoli declined to comment, saying they were collecting information on what happened.
Three prominent aid groups are suspending their migrant rescue efforts in the Mediterranean Sea after receiving threats from the Libyan coastguard.
The Spanish NGO Proactiva Open Arms announced Tuesday evening via social networks that its ship, Blue Gulf, had been seized for two hours by the Libya coastguard in worldwide waters and forced to head to Libyan ones. There have been numerous incidents involving encounters between humanitarian vessels and the Libyan coastguard. "There is a strategy of dissuasion and intimidation, and strong pressure by the Libyans in order for (NGOs) to stop operating at sea", Luigi Manconi, head of the Italian Senate committee for Human Rights, said on RAI state broadcaster.
Italy has drawn up a Code of Conduct setting stricter rules on how the groups can operate, but only five out of eight NGOs have signed it. Some 97,000 migrants have reached Italy so far this year.