During a media briefing on Thursday, police officials asserted that some demonstrators were armed with knives and refused to follow instructions, and that officers feared for their lives and opened fire.
Two civilians were killed in the capital, Hargeisa, and the third in Erigavo town in the Sanaag region.
The protests occurred in major towns across Somaliland, the northern region that separated from Somalia three decades ago and seeks recognition as an independent country. They were called by the two main opposition parties, UCID and Wadani, which have asked President Muse Bihi Abdi not to delay the presidential election scheduled for November 13.
The opposition parties are concerned about the management of the election and the registration of political organisations. The Somaliland government allowed the protests to occur in six regions but in limited areas, which the parties opposed.
Witness Idris Hassan confirmed to The Associated Press one death in Hargeisa after the demonstrators clashed with security forces. The governor of the Sanaag region, Ahmed Abdi Muse, confirmed the Erigavo death to local media.
Internet service was briefly cut off in Somaliland on Thursday morning.
The US Embassy in Somalia said it "strongly" urged Somaliland's ruling and opposition leaders to avoid violence in demonstrations and "return quickly to political dialogue." It warned that a failure to agree on the election threatens Somaliland's "achievements in democratic governance."
The head of the British Office in Hargeisa, Lizzie Walker, also urged peace and dialogue.
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