Biometric machines failed to identify voters and election materials arrived late at some polling places, the BBC reported.
Many voters were unable to cast ballots Friday, so officials decided to extend voting into Saturday.
Eight presidential candidates are on the ballot, including incumbent leader John Dramani Mahama and opposition front-runner Nana Akufo-Addo, the son of a former president, CNN reported.
In addition to the presidential election, 275 parliamentary seats are up for grabs in the election.
Before voting was extended, the electoral commission said it expected to declare a winner -- should one candidate have a majority -- within 72 hours after polls close Friday.
"Ghana has organized five previous successful elections, and there should not be any reason why this year's election should not be successful," the president said in a statement.