In the presidential race, Yoweri Museveni, 81, in power since 1986, is seeking a seventh successive victory as he faces a challenge from Bobi Wine, a charismatic pop star, aged 43.
Where voting has been taking place, there are reports that the biometric machines used to verify voters’ identities are still malfunctioning in some areas.
“Some biometric machines are not working. I don’t know if it’s the internet,” a ruling party official told AFP news agency.
Delays have also been caused by polling materials and equipment failing to arrive at some stations on time.
Casting his vote in his native Rwakitura Village in the western Mbarara region, Museveni said he had also experienced difficulties.
“I put my thumbprint on the machine but it did not accept it. However, my face was accepted instantly by the machine. The machine works,” he said.
Asked if he would accept the election outcome, the president said: “This is one of the manipulations – we have to find out why, what was the problem?”
“We are now verifying whether this was deliberate,” he added.
Election chief Simon Byabakama ordered the use of the national voters’ register where biometric machines failed to function.
“It is the primary duty of the Electoral Commission to ensure that no citizen is disenfranchised due to machine failure,” he said.
The problems appear to be affecting both areas seen as pro-government as well as those seen as opposition strongholds.
The country’s law allows polling hours to be extended if challenges disrupt the voting process.
“Polling stations will remain open until all registered voters in the queue by 4:00 pm (13:00 GMT) have cast their votes,” said Byabakama.
The presidential poll is essentially a two-horse race between Museveni and Wine, but given the president has won the six previous elections, analysts say he is likely to further extend his time in power.
Wine has promised to tackle corruption and impose sweeping reforms, while Museveni argues he is the sole guarantor of stability and progress in the country.
The result of the presidential vote will be announced by 16:00 local time (13:00 GMT) on Saturday, the electoral commission has said.
