An agent for longtime opposition leader and candidate Raila Odinga announced from the lectern on Saturday that the tallying centre was the "scene of a crime" before calm was restored.
The agent, Saitabao Ole Kanchory, offered no evidence in the latest example of the unverified claims that both top campaigns have made as Kenya waits for official results.
The electoral commission has seven days from Tuesday's election to announce results.
Chair Wafula Chebukati on Saturday again said the process was too slow, and the commission told non-essential people watching at the center to leave.
Police remained at the centre on Sunday morning.
The race remains close between Odinga and Deputy President William Ruto as the electoral commission in Nairobi physically verifies more than 46,000 results forms electronically transmitted from around the country.
Turnout dipped sharply in this election, to 65 per cent, as some Kenyans expressed weariness with seeing long-familiar political leaders on the ballot and frustration with economic issues including widespread corruption and rising prices.
Outgoing President Uhuru Kenyatta crossed the ethnic lines that have long marked politics by backing Odinga. The president fell out with his deputy Ruto years ago.
Past elections have been marked by political violence, but civil society observers, police, religious leaders and others have said this one has been peaceful.
US Secretary of State Antony Blinken in a call with Kenyan President Uhuru Kenyatta on Saturday "encouraged continued peace and patience as the vote tallying from Kenya's August 9 election proceeds", spokesman Ned Price said.
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