Most of the livestock deaths were reported in Tog-Wajale district where the mayor, Omar Aden Gazali, said at least 5,700 animals died after it rained for 72 hours.
Gazali said two people had died in the floods, more than 100 families (600 people) were displaced and homes and business premises destroyed.
The mayor said most of the families who lost their livestock came from the eastern parts of Somaliland in search of pasture.
Gazali said a bridge connecting the town to neighbouring Ethiopia was inundated with water and almost destroyed.
"The police started to stop people from crossing the bridge between the two sides of the town," he said.
Said Mohamed Ahmed, the mayor of Wajale, on the Ethiopian side, said the floods had also affected their part of town.
"We sent our teams to survey the problems caused by the rains; there is a lot of damage caused by the floods," he said.
Khadar Abdi Hussein, a local resident, said the flooding of Wajale river, which is seasonal, had also reportedly displaced hundreds of families in Gabiley region, including Ged-baladh vilagge, Allaybaday District.
Hussein said many animals weakened by a prolonged drought had succumbed to the rains. "They were too weak to survive," he added.
The floods come days after Somaliland officials said the east of the region remained drought-stricken.
Mohamoud Awed Du'alle, the deputy mayor of Erigavo, the region's capital, had earlier told IRIN the situation was deteriorating in Jiidali, 35km southeast of Erigavo, and Yufle, Goofa and Booca areas, where cattle and sheep had already started dying.
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