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A young woman was found unconscious on one of the vessels and later died, the group said.
Some 412 people were crammed onto a single wooden boat, while the others were picked up from huge inflatable dinghies, which had set sail from the coast of Libya.
The weekend rescues mean that about 22,000 mainly African migrants have been picked up heading to Italy so far this year, while around 520 have died trying to make the crossing.
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| Nearly 1,200 migrants picked up off Libya, heading to Italy. |
An Italian prosecutor said last week that humanitarian ships operating off Libya were undermining the fight against people smugglers and opening a corridor that is ultimately leading to more migrant deaths.
The chief prosecutor of the Sicilian port city of Catania, Carmelo Zuccaro, said he also suspected that there may be direct communication between Libya-based smugglers and members of charity-operated rescue vessels.
Non-governmental organizations deny any wrongdoing, saying they are simply looking to save lives, but they are facing criticism in Italy, which has taken in about half a million migrants since the start of 2014.
A parliamentarian with the right-wing Northern League party on Sunday accused the NGOs of acting as a "taxi service", bringing migrants straight to Italy rather than to closer nations, such as Tunisia and Malta.
"If the government does not decide to put a brake on these NGO boats, we will find ourselves overrun by tens of thousands of African immigrants by the end of the year," lawmaker Paolo Grimoldi said.
Migrants who have come this year have told of increasing violence and brutality in Libya, where rival factions battle for power and people smugglers operate with impunity since the 2011 overthrow of former leader Muammar Gaddafi.
