But refugee advocates have in return accused Italy of being complicit in human rights abuses, by sending navy vessels into Libyan waters to turn back migrant boats.

Refugee advocates deny accusations that non-government organisations have formed a "taxi service" for migrants fleeing Libya, saying instead they are providing a vital search-and-rescue service that is saving thousands of lives.

Italian coastguards confiscated the boat, named Iuventa and operated by activist collective Jugend Rettet??????, on the island of Lampedusa after receiving evidence that its crew were in communication with people smugglers.

"The evidence is serious," Ambrogio Cartosio, chief prosecutor in the western Sicilian city of Trapani, said.

"We have evidence of encounters between traffickers, who escorted illegal immigrants to the Iuventa, and members of the boat's crew."

He said nobody had been charged but his investigation was continuing. He also said it would be a "fantasy" to say there was a coordinated plan between the NGOs and the Libyan traffickers.

Jugend Rettet did not respond to a request for an interview from Fairfax Media.

On Twitter on Thursday they said their crew were interviewed by officials "as part of the standard procedure" and they had received no information about an investigation.

"Our legal teams are working hard to examine the legal basis of the confiscation of the ship," they said.

They watched their ship's forced departure from Lampedusa "with heavy hearts" because the ship was "dearly needed", they said.

Last month, Italy, with the backing of the European Union, imposed a code of conduct for NGOs in the Mediterranean.

Jugend Rettet said they had been negotiating with Rome over the code, but on Tuesday had decided not to sign it until it was rewritten.

"Our top priority is to save people in distress but this is not prioritised [in] this code of conduct [which] would legally put us in an uncertain position," they said in a statement on Facebook.

In May, Cartosio told a parliamentary committee in Rome that he had become suspicious of NGOs after noticing some rescue crews seemed to know in advance where to find migrant boats, and were making rescues without informing the Italian coastguard.

Carmelo Zuccaro the chief prosecutor of the Sicilian port of Catania, has claimed he had evidence of phone calls between people smugglers and aid groups, but in May admitted he was expressing only a "hypothesis" and had no proof that could be used in court.

A fleet of around a dozen boats crewed by humanitarian groups are working on the Mediterranean to perform rescues.

Around 85,000 migrants arrived in Italy by boat in the first six months of 2017, 21 per cent more than in the same period in 2016.

More than 2200 people have died attempting the crossing this year, according to the International Organisation for Migration.

Last year, rescues in the Mediterranean were closer to Italy, but now they were happening much closer to the border between Libyan and international waters, prompting accusations the NGOs are encouraging people smugglers.

Smugglers were "including the presence of NGO boats in their business model", a European official familiar with the situation told Fairfax Media last month.

Izza Leghtas, a senior advocate for Refugees International, said search and rescue should not be made into a political issue.

NGOs performed more than a third of the rescues in the area in the first part of 2017, Leghtas said.

"They are filling a huge gap??? if they weren't doing that work then we would be talking probably about thousands more people drowning."

"They are proactive, they go to the areas where they know people are at risk in international waters," she said, while official boats were more focused on border control. "We are talking about life and death situations and that needs to be the priority."

Part of the problem was the pressure Italy was coming under because other European countries, including Italy's closest neighbours, had not stepped up to take a share of the migrants and refugees arriving from Africa.

The Italians had been traumatised by the number of deaths at sea and felt they had been left alone to handle it, Leghtas said.

She rejected the claim that NGOs were encouraging migrants to take to the sea.

"The conditions in Libya are so horrific, it's a question of a push factor not a pull factor," she said. "People get out of Libya because it's unbearable, because people are killed and tortured and sexually abused.

"To focus on the rescue operations and ignore the fact they are fleeing for their lives [is wrong]??? people are going to go regardless [of the NGO boats]."

She said her group was deeply concerned by the Italian government's plan to send its vessels into Libyan territorial waters to help the Libyan coastguard intercept migrant and refugee boats.

"It is no secret that migrants and refugees who are intercepted and returned by the Libyan coast guard face horrific abuses in Libya's migrant detention centers," said Leghtas. "By engaging in these operations, the Italian government would be knowingly complicit in these abuses."