All day Saturday, the Iuventa, a ship operated by the German NGO Jugend Rettet, had searched through deep fog for a vessel in distress after receiving an alert from the Italian coastguard.
On Sunday morning near Zuwara, in northwestern Libya, the crew spotted a dinghy which did not appear to have been in the water for long.
It also lacked the standard markings left by search teams to signal that the ship's passengers had been rescued.
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"We can't be sure that it's the boat we were looking for but... we have to suppose that there was an accident," said Pauline Schmidt, a spokeswoman for the NGO.
The dinghy was typical of those used by traffickers bringing migrants to Europe, often packing 120 to 140 people on board.
The Iuventa's crew found no survivors or bodies in the area. The passengers may have been rescued by Libyan fishermen, but the International Organization for Migration, which keeps tallies of the migrant rescue in Libya, said it had not registered any such operation.
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It also said it had been informed that bodies had been discovered on a beach about 30 kilometres from Zuwara, though it had not been able to verify the accounts.
Over 1,000 migrants are feared to have died in waters between Libya and Italy so far this year, according to the migration agency, while nearly 37,000 have been rescued and brought to Italy.
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