The organisation was among those which refused to sign a ‘code of conduct' on migrant search and rescue operations in the Mediterranean imposed by the Italian government.
The ship, Iuventa, was escorted by the coastguard to the port of Lampedusa, an island that lies between Sicily and Tunisia.
Two Syrians, who had been transferred to the ship by one of the Italian military units employed in rescue operations, were taken to the island's reception centre, Ansa reported.
Paolo Monaco, Lampedusa's port authority chief, said the move was part of “a routine check”.
“It will not lead to any problem,” he was quoted by Ansa as saying.
“We will now control the documents of the whole crew and this morning they will already be able to leave Lampedusa if everything is in order.”
Only three of nine NGOs signed the new protocol on Monday.
Among those who refused was the medical charity Doctors Without Borders (MSF), which said two sticking points prevented it from doing so.
One was the obligation for rescue vessels to operate with an Italian police official on board, and the other was the ban on moving rescued migrants from one aid vessel to another at sea, which complicated missions.
The code, created to address the biggest migrant phenomenon in Europe since World War II, lays down 13 rules Rome insists must be followed to prevent aid groups rescuing migrants from acting as a magnet for human traffickers.
But the rules have been widely criticised by the NGOs as making it more difficult for them to save the lives of those attempting the perilous crossing from the shores of crisis-hit Libya to Europe.
The interior ministry said those who "refuse to agree and sign are excluded from the system of sea rescues".
Titus Molkenbur, a spokesperson for Jugend Rettet, sad on Monday that the privately-funded aid organisation “we would only sign if the new rules made our work more efficient and increased the security of our volunteers."
The new rules, which have been given a green light by Brussels, forbid NGOs from sailing into Libyan waters unless lives are at risk, or communicating with smugglers - including using lights that could attract traffickers.