"There is an Italian code of conduct that aims to avoid these situations," said European Commission spokesperson Natasha Bertaud.
"We call on all parties to respect it in future," she added.
The European Commission was "closely following" the case and EU Migration Commissioner Dimitris Avramopoulos had spoken to Itay's Interior Minister Marco Minniti about it, Bertaud said.
Bertaud's remarks came after Italian prosecutors seized a ship run by the Proactiva Open Arms NGO when it docked in the Sicilian port of Pozzallo on Saturday with 216 people aboard after declining a request to hand over all women and child migrants on board to Libyan coastguard.
Prosecutors in Catania are also probing the charity ship's captain and two of the NGO's officials over the incident, during which Proactiva Open Arms alleges that Libyan coastguard threatened to open fire on the vessel unless its crew handed over the passengers.
Italian coastguard gave the NGO permission to land in Sicily but said they should have asked Spanish authorities for advice on where to go, and noted that Malta was closest port for them.
The Italian government introduced in July last year the controversial code of conduct in a bid to curb the activities of charity rescue ships operating in the Mediterranean.
With EU support, Italy also gave equipment and training to Libyan coast guard aimed at strengthening their capacity to intercept migrants before they are rescued by NGO vessels.
Most migrants who embark on dangerous sea journeys to Europe are anxious not to be taken back to Libya, where they face widespread abuse and torture in the lawless country's detention centres.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
