As voting concluded yesterday, provisional results gave the 71-year-old leader 63 per cent of the vote with nearly half of polling centres counted.
His chief rival Kizza Besigye -- in second place with 33 per cent -- was arrested again yesterday after police stormed his party headquarters in the capital.
The police raid came as people continued to vote at dozens of polling stations in the wider Kampala area, where voting was extended in 36 sites for a second day after delays on Thursday that Commonwealth election observers called "inexcusable".
The former rebel fighter faced a challenge from seven candidates, but is expected to win re-election for a fifth term in office and extend his 30-year rule of the east African country.
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Thursday's presidential and parliamentary votes were disrupted in the capital Kampala by the late arrival of ballot boxes and papers, angry demonstrations by frustrated voters and police using tear gas.
Besigye, who was arrested during campaigning on Monday and again on Thursday evening, was taken into custody for a third time yesterday.
Police surrounded Besigye's Forum for Democratic Change (FDC) headquarters, firing tear gas and water cannon, before bursting inside and arresting top party officials.
"Some reasonable measures have been applied to rein in FDC supporters who wanted to disturb the peace and the ongoing exercise," said senior police officer Felix Andrew Kaweesi.
He accused Besigye's FDC of planning to publish its own tally of results, contravening electoral law.
"(Kerry) urged President Museveni to rein in the police and security forces, noting that such action calls into question Uganda's commitment to a transparent and credible election process free from intimidation," the State Department said in a statement.