Electoral Commission's spokesperson, Paul Bukenya, said some of the machines had failed to work as they were deployed to confirm the details of prospective voters waiting to cast ballots at polling stations.
The personal details of voters are first verified by the machines before they are cleared to cast their votes.
Voting in Uganda began as early as 7am and will close at 5pm according to the electoral commission's polling day schedule.
Despite the violence and tension in the lead up to the vote, there has been no heavy security presence as anticipated in the streets of Kampala and other cities.
18, 103,603 Ugandans have been registered to vote in 34, 684 polling stations spread across the country of over 46 million people.
The arrival of voting materials had been delayed, some reaching polling stations more than 30 minutes before polling was supposed to begin.
In power since 1986, veteran leader Yoweri Museveni, 76, is bidding for a fifth term in office but faces a tough contest from 38-year old Bobi Wine, a pop star turned politician.
The outcome of the polls will be announced in the next few days.