"There have been two deaths today in circumstances yet to be established," said spokesman Albert Damantang Camara.
"The two were killed by police during clashes with youths in Hamdallaye district," an opposition fiefdom in the capital Conakry, a security source said.
Demonstrators gathered less than a week after at least 50 people were arrested over an arson attack that killed five children, in post-election violence in central Guinea.
With around half of the results from 342 communes now declared, the independent electoral commission Ceni put the party of President Alpha Conde neck and neck with that of opposition leader and former prime minister Cellou Dalein Diallo.
The vote was the first of its kind since a military dictatorship ended a decade ago and followed eight years of delays blamed on a lack of funds, political infighting and the 2013-16 Ebola crisis.
Mohamed Ibn Chambas, special representative for the United Nations Secretary-General in the area, said in a statement Monday after a five-day visit to Conakry it was "fundamental for the Ceni to be able to carry out its work calmly and serenely."
He urged rival factions to put aside their "discourse of hatred, acts of violence and violations of freedoms and fundamental rights."
The Economic Community of West African States also urged an end to the violence on Sunday.
The resumption of a strike by teachers meanwhile drew widespread support in Conakry and several provincial cities, according to teachers and witnesses interviewed by AFP, though the government said the dispute was mainly confined to primary and secondary schools.
Several trade unions had also threatened a nationwide "general strike" if the striking teachers were punished.
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