Official tallies late on Friday showed Museveni winning 63% of Thursday's vote to Kizza Besigye's 34% with nearly 60% of polling stations reporting.
The latest partial figures made it all but mathematically impossible for Besigye to win but left open a slim chance of a run-off if Museveni's totals fall to below 50% when all results come in.
But Museveni's National Resistance Movement, NRM, said an internal canvas of polling stations in 63 of 69 districts showed its candidate winning with the same percentage announced by Uganda's Electoral Commission.
NRM spokesman Ofwono Opondo said: "We have won this election,"
"We have won both the presidential and parliamentary vote."
The official numbers showed the president well on his way to a third elected term in office, extending his 20-year hold on power with a new five-year mandate.
Besigye's Forum for Democratic Change, FDC, alleged "serious irregularities" on polling day and in vote reporting and accused authorities of issuing returns slowly to "cook results in favour of President Museveni".
FDC chairman Sulaimani Kiggundu told reporters: "We will question the final results if we see irregularities in the way they have been announced. We will reject them."
Badru Kiggundu, the Electoral Commission chairman, denied any malfeasance, saying any such charge was "non-factual" as he announced the latest returns.
"We will question the final results if we see irregularities in the way they have been announced. We will reject them"
Chairman of opposition Forum for Democratic Change
The EU Election Observation Mission also said the polls had been fraught with flaws and warned of post-election violence, citing deep voter fears that clashes would erupt as the counting continues.
It said there had been "significant bias" against Besigye and other FDC candidates in the state-run media and that Museveni's ruling National Resistance Movement used government resources to boost its support.
Final returns are due Saturday.