Two survivors of sinking said traffickers rammed boat, which left Egypt on 6 September, after passengers refused to transfer vessel

About 500 migrants are feared to have drowned after the boat carrying them from Egypt to Malta was apparently rammed and deliberately sunk by people-traffickers, an intergovernmental group has said.

The news – based on the accounts of two Palestinian survivors – emerged on the same day up to 200 more people were feared dead when another boat heading to Europe capsized off Libya.

The Geneva-based International Organisation for Migration (IOM) said there was no independent verification for what happened to the vessel heading to Malta, mainly because only nine people are believed to have survived. The IOM's account comes from the two Palestinians, who were rescued by another boat and taken to Sicily.

Malta's armed forces said it had flown seven survivors, who were suffering from hypothermia, to a hospital in Crete. It said initial information pointed to a collision of some sort between a boat carrying up to 400 migrants and another vessel.

If the Palestinian men's account is correct, by the IOM's tally about 2,900 migrants have died this year in the Mediterranean against 700 for all of 2013. "If this story, which police are investigating, is true, it would be the worst shipwreck in years – not an accident but a mass murder, perpetrated by criminals without scruples or any respect for human life," the IOM said in a statement.

The UN High Commission for Refugees said the situation in the Mediterranean was unclear and it was trying to get confirmation of five shipwrecks. A spokeswomanfor the UN High Commission for Refugees, Carlotta Sami, described it as "without any doubt the deadliest weekend ever in the Mediterranean" and the agency said it believed at least 500 were dead or missing in the last three days.

Leonard Doyle, an IOM spokesman, said the Palestinian men recounted having boarded the people-smuggling vessel in Damietta, Egypt, on 6 September. Midway through the voyage the people-smugglers, who appeared to be travelling in a separate boat, ordered the migrants, who also came from Syria, Sudan and Egypt, to switch to a smaller, less seaworthy vessel. The migrants refused to do so.

Doyle said: "The survivors said the traffickers became so enraged after the migrants refused to board the replacement craft, there was an argument, a fight, and that the smugglers used their boat to sink the one the migrants were on. It seems they intentionally rammed the ship."

One of the Palestinian man, aged 27, said he was able to cling to a lifebuoy for a day and a half, initially with around six other passengers.

Doyle said: "Over the next 24 hours they all disappeared. The man said that among these was one young Egyptian who said he had left home to earn money and pay for the heart medicine of his father."

The survivor was eventually picked up by a Panama-registered container ship that was already carrying 386 survivors from another sunk migrant boat, and taken to Sicily. The same ship seemingly picked up the other Palestinian man, who is aged 33. The IOM has not spoken to the other seven survivors.

The IOM learned of the men's account over the weekend and sent an Egyptian investigator to speak to them. A spokeswoman for the Italian coastguard said it had no information on the apparent sinking as it had not had contact with any survivors. A search of the area had uncovered no trace of a boat or any bodies, she added.

Earlier on Monday, the Libyan navy said a migrant boat carrying around 250 people capsized off the coast near Tripoli. While 36 people were confirmed rescued, many others were feared dead.

A navy spokesman, Ayub Qassem, told Reuters the boat had sunk near Tajoura, east of the capital, Tripoli. He said: "There are so many dead bodies floating in the sea."

Doyle said the IOM had not previously heard of so many migrants drowning by a deliberate sinking, but that if it had happened it was possible no one survived. "On the face of it it's looking like a horrific incident," he said.

Huge numbers of people are attempting to flee from Africa to Europe, with numbers sharply up this year, in part due to the continued violent chaos in Libya and Syria. More than 100,000 people have been rescued since January, the UNHCR, says.

According to the agency that monitors the EU's external borders, more migrants are likely to risk the dangerous crossings this year than at the height of the Arab spring.

By mid-August this year there had already been almost as many illegal border crossings counted as there were in the whole of 2011, when the number reached 140,000, said Frontex.

Doyle said the situations in Libya and Syria were undoubtedly part of the reason for the increased deaths, with "desperate" migrants willing to try the crossing in almost any vessel. "They're very much at the mercy of traffickers," he said.

Earlier this year a leading Libyan people smuggler, speaking anonymously to the Guardian, explained how he uses a different tactic to ensure the trafficking boat can be used again.

The man said that once the Italian military was en route to the ship he and his crew would decamp to a small rubber inflatable. Once the migrants are removed they return to the smuggling boat and return in it to Libya.