Somaliland broke away from Somalia in 1991 and operates as an independent state but has not won international recognition.
"The death toll from the cyclone is so far over 50 people," vice president Abdirahman Abdullahi Ismail told reporters late on Tuesday in Somaliland's capital Hargeisa. "(The) death toll may rise because there are other people who are still missing."
Tropical cyclone Sagar made landfall on Saturday in north-western Somaliland and Djibouti, three days after it formed in the Gulf of Aden, according to the U.N. Office for the Coordination of Humanitarian Affairs (UNOCHA).
UNOCHA said 669,000 people have been affected in Somaliland, giving a toll of 25 people so far confirmed dead and 27 missing, with numbers likely to rise as information arrives from areas that are now inaccessible.
Two people were confirmed dead in Puntland, a semi-autonomous northeastern region of Somalia, and another two in Djibouti, UNOCHA said.
"80 per cent of livestock in affected areas were killed. Reports indicate that some 700 farms have been destroyed in Somaliland," UNOCHA said.
Conflict in the disputed regions of Sool and Sanaag was making it harder to reach some flood-hit areas, UNOCHA said earlier this week. Drought dating back to 2015 has made the regions prone to flash flooding after rain.
Vice president Ismail said assistance from the United Arab Emirates had allowed authorities to reach affected areas and bring emergency food.
"Using the two helicopters UAE helped us with, we have reached today Lughaya and Baki towns which were hit by the cyclone," he said. "There are other far areas we flew over but could not land and reach because of floods."
The UAE is an important aid provider for Somaliland, where a firm owned by the gulf state has pledged up to $440 million to develop the breakaway's region port of Berbera.
Speaking separately, Somaliland's president Musa Bihi said the region needed emergency help: "Over 600 people lost their homes, animals and farms," he told students in Hargeisa.
Since the beginning of the rainy season in Somalia in March, riverine and flash floods have caused fatalities, massive displacement and damage to infrastructure and cropland. An estimated 772,500 people have been affected by flooding and more than 229,000 are displaced, UNOCHA said.
After a severe drought last year, East Africa has been hit by two months of heavy rain, affecting nearly a million people in Kenya, Somalia, Ethiopia and Uganda.