Foreign affairs spokesman Daniel Kabuto said there were "technical problems" concerning the exact role of the mission, saying it does not have the authority to verify the final results, something it says can be done only by the electoral commission, known as Ceni.
"We asked for an election observation mission, not for a validation of the elections," Kabuto told AFP. "For the government, the validation of elections is the prerogative of Ceni, it's very clear, there can not be any debate about that."
Burundi, a small nation in Africa's Great Lakes region, emerged in 2006 from a brutal 13-year civil war and its political climate remains fractious ahead of the polls.
President Pierre Nkurunziza, in power since 2005, is expected to run for a third term in office despite opponents' claims that that would violate Burundi's constitution.
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"Elections are being held at a crucial time in the history of Burundi," UN election observer chief Cassam Uteem said, a former president of the Indian Ocean island of Mauritius.
A series of recent attacks -- including a five-day battle between the army and a rebel force that entered the country from neighbouring eastern Democratic Republic -- comes amid mounting tensions ahead of the polls.