Hundreds of Somalis are feared to have drowned in the massive waves produced by Sunday's undersea earthquake off the coast of Indonesia.
Beaches in Kenya have now reopened
A government spokesman said settlements along Somalia's coast had been flooded by the rising waters.
"Coastal towns have been swept away by the waves and there is severe damage to property," Yusuf Ismail said.
Waves which swept 7,000km (4,000 miles) from the epicentre, also struck Kenya, Mauritius, Reunion and the Seychelles.
About 100 Somali fishermen have not returned after putting out to sea on Sunday.
"The bodies of 48 people have been recovered," rural development minister in Somalia's north-east state of Puntland, Ali Abdi Awari, told BBC News.
Somali elders gathering information on two-way radios and local journalists put the death toll at more than 50 people, although Mr Ismail said the deaths on land alone in the central and north-eastern areas could be "in the hundreds".
The government - which is currently based in Kenya as it is considered too dangerous for ministers to return to Mogadishu - has called for aid.
In the Kenyan port town of Malindi, where a 20-year-old swimmer reportedly drowned, fishermen ventured back in the water on Monday to gather the remains of their boats.
Beaches that were closed on Sunday reopened, amid government warnings to tourists to take precautions.
There was also damage in the Seychelles where a bridge linking the main airport and capital Victoria was destroyed while a village in northern Mauritius was submerged for almost three hours following the surges.
"I am asking people to remain calm and help those in need," Seychelles President James Michel said in a television address.
About 15 fishing boats were damaged in the French territory of Reunion.
Officials in Tanzania and its semi-autonomous
Zanzibar and Pemba islands are giving hourly warnings, advising fishermen to look out for more waves.
The British government warned its citizens in Madagascar, Mauritius, the Seychelles, Kenya and Tanzania to be alert for potential danger from the sea surges.