With about a third of the votes counted, preliminary results indicated Kenyatta was ahead of Prime Minister Raila Odinga, 55 percent to 41 percent, The New York Times reported.
Voters voted overwhelmingly along ethnic lines, with some areas voting 98 percent for the leader from their ethnic group, preliminary results indicated.
The Times said many businesses in Nairobi were closed Tuesday over concern about rioting once the results were announced.
Kenyatta, a deputy prime minister, is accused of financing death squads that killed women and children following Kenya's 2007 presidential election that devolved into ethnic fighting in which at least 1,000 people died.
Kenya's election commission has been tabulating the votes since polls closed Monday and said they expected preliminary result by Wednesday.
Inspector General of the Kenya Police David Kimaiyo said several suspects were arrested in a rash of pre-election attacks along the country's coastal region in which six police officers were killed.
Kimaiyo said more suspects remained at large, adding, "We will catch them."
Grocery store shelves were stripped of food and other staples as people stocked up in case rioting erupted, while many fled ethnically mixed urban areas fearing reprisal killings, the Times said.
"We must keep the peace," said William Ruto, Kenyatta's running mate.
Ruto also has been charged by the International Criminal Court with crimes against humanity, accused of orchestrating widespread violence following the 2007 election.