President Yoweri Museveni, who has led Uganda since a rebel group he was aligned with seized power in 1986, won 71% with a fifth of the votes counted. Challenger Kizza Besigye had 22%.
"There have been widespread malpractices in the electoral process," Besigye said.
He said voters had been bribed and that "huge amounts of money" landed in the hands of polling agents and candidates to pay off electoral officials.
The government has dismissed the accusations and said the opposition is trying to undermine the election.
A new term would give Museveni five more years in power. Final results will be released on February 20.
Museveni has already vowed to quash any Egypt-inspired uprisings aimed at toppling entrenched regimes.
Ugandans lined up early to cast their ballots amid heavy security in the capital and other areas. Increased security forces in anti-riot gear patrolled the streets of Kampala a day after the elections.
Parliament removed presidential term limits in Uganda five years ago, essentially allowing the incumbent to run for office indefinitely.
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