The crew of the Dutch-flagged ship had expected the vessel to be detained or impounded as a show of strength from Italy's far-right Interior Minister Matteo Salvini, who says charity rescue boats aid illegal migration.
“As assumed, we are blocked for political reasons! There was high pressure on the coast guard to find a reason to chain us,” Sea Watch International said on Twitter.
“They can chain our ships, but they can´t chain solidarity!” it said.
Officials boarded the ship on Thursday after it disembarked 47 migrants rescued in the Mediterranean “to perform a technical inspection of conditions on board”, the coast guard said.
“During the inspection of the Sea Watch 3, a vessel certified as pleasure yacht, a series of non-compliances concerning both navigation safety and compliance with rules protecting the marine environment were noted,” it said.
The coast guard will “not permit the departure of the ship until they are resolved,” it added, without providing further details.
Sea Watch's mission head Kim Heaton-Heather told AFPTV on Thursday that he feared “problems with the authorities”.
“But I am also very, very certain that in the end, no matter what allegations are brought against the organisation, the ship or the crew as whole, none of these allegations will stick and the truth of the matter will come out,” he said.
Salvini, who is looking into whether it is possible to ban charity rescue ships from Italian waters, accuses the Sea Watch crew of sailing straight for Italy rather than taking the migrants to closer ports in Libya or Tunisia.
The German charity says it tried but failed to get a response from Tripoli or Tunis and had no other option than to head to Italy.