At least 104 bodies have been pulled out of the waters near the western city of Zwara but the expected death toll is likely to be higher since such boats usually carry up to 125 people.
Colonel Ayoub Gassim said the Libyan coastguards found the empty boat late on Thursday and it is possible the boat capsizedsome time earlier.
He blamed Europe for “doing nothing but counting bodies” to stop the illegal migration from Libya.
The discovery of the bodies off Zwara is the latest in a string of tragedies that have claimed more than 1,000 lives in recent weeks as desperate migrants embark on treacherous sea journeys seeking a better life in Europe.
Four bodies were recovered and 340 people rescued today from a sinking migrant boat carrying a “significant number” of people in the Mediterranean Sea south of the Greek island of Crete.
The coastguard said the 25-metre vessel, which resembled a large fishing boat, had been carrying an undetermined number of people when it was located half-sunk about 75 nautical miles south of Crete in international waters, and within Egypt’s search and rescue area of operation.
Most survivors will be transported to Italy, with others to be taken to Egypt, Malta and Turkey, the coastguard said.
Greece was sending two patrol vessels, a military airplane and three helicopters, while five passing ships were participating in the rescue operation and one more was on its way.
The coastguard said the operation was continuing to locate any potentially missing passengers from the migrant boat.
“The information we have on the number of people on board the vessel is still unclear – we’ve heard that there were 400 or 500 people on board, but we cannot confirm that number,” coastguard spokesman Nikos Lagadianos said.
Migrant smugglers have opted for more dangerous routes after a March agreement.
The short crossing from the Turkish coast to Greek islands was the preferred route for migrants heading to Europe until Balkan countries closed their borders and the European Union reached an agreement with Turkey to stem the flow of people.
Under that deal, those arriving on Greek islands from 20 March onwards face deportation back to Turkey unless they successfully apply for asylum in Greece, a financially troubled country few migrants or refugees want to stay in.