"Kizza Besigye has been arrested from our HQ and taken to (an) unknown location," his Forum for Democratic Change (FDC) party said.
Police today surrounded the FDC headquarters in the capital's Najjanankumbi district, firing tear gas at crowds of opposition supporters. They also used water cannons to fire blue-coloured water to break up the demonstrations.
"Some reasonable measures have been applied to rein in FDC supporters who wanted to disturb the peace and the ongoing exercise," senior police officer Felix Andrew Kaweesi told AFP, adding that the arrests came amid fears Besigye was to publish FDC tallies of polling.
Besigye, 59, Museveni's former personal doctor, is making his fourth run at the presidency and ended his campaign by saying the election would be neither free nor fair.
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Police then stormed the building, arrested Besigye and other top party officials.
Besigye was arrested on Monday during campaigning, and again on Thursday evening after polling. He has been repeatedly detained by police in the past, and is commonly released without charge hours later.
Preliminary results released by the Electoral Commission from just over a third of polling centres nationwide have given the 71-year-old incumbent President Yoweri Museveni a clear 63 per cent of the vote.