Italian President Sergio Mattarella had said earlier on Monday that several hundred people appeared to have died in a new tragedy in the Mediterranean, after unconfirmed reports spoke of up to 400 victims of capsizing near Egypt's coast.
More than 1.2 million African, Arab and Asian migrants have arrived in the European Union since the start of last year, many of them setting off from North Africa in rickety boats that are packed full of people and which struggle in choppy seas.
"We have no fixed number but it is between 200 and 300 Somalis," Mohamed Abdi Hayir, Somali information minister, told Reuters by telephone when asked about possible Somali deaths in the latest incident.
Another Somali government statement, which offered condolences, put the number at "nearly 200", saying they were mostly teenagers. It said the boat they were on had capsized after leaving Egypt.
"There is no clear number since they are not travelling legally," the minister said, adding that he understood the boat might have been carrying about 500 people, of which 200 to 300 were Somalis "and most of them had died".
He did not give a precise timing for the incident.
One year ago, an estimated 800 migrants drowned off the Libyan coast when the fishing boat they were travelling in collided with a vessel that was attempting to rescue them - the most deadly Mediterranean shipwreck in decades.
Egyptian, Italian and Greek officials had earlier been unable to confirm the report of a new sinking.
A UN refugee agency official told Swiss broadcaster SRF he knew of 40 survivors from what appeared to be the same incident.
"We know there are 40 survivors and that as many as 460 people may have been on the boat who sailed from Egypt," the UNHCR's Beat Schuler told the broadcaster in what it said was a report from Malta.
In an article on the Somali National News Agency website, President Hassan Sheikh Mohamoud on Monday "sent his heartfelt condolence on his behalf and on behalf of the citizens of Somalia to the families who lost their loved ones".
The president urged Somalis to stand together in helping "stop such hazardous trips to overseas".
Somalia has a large diaspora, with many Somalis in Europe and the United States, after fleeing two decades of conflict. The Western-backed government is seeking to rebuild the Horn of Africa nation but is still battling an Islamist insurgency.
Islamist al Shabaab rebels often carry out gun and bomb attacks, particularly in the capital Mogadishu, where some hardy Somalis business people are returning to from abroad to invest.