The Islamist militants were suspected of killing seven in separate attacks in northeastern Gombe state, including at polling stations, while on Friday, 23 people were beheaded in Borno.
President Goodluck Jonathan was the most high-profile victim of the glitches with handheld readers, which scan biometric identity cards to authenticate voters to help cut electoral fraud.
The 57-year-old, who is seeking a second term of office, was forced to abandon his attempt to accredit for the ballot in his home town of Otuoke, Bayelsa state, after the device repeatedly failed.
The Independent National Electoral Commission (INEC) accepted there had been "challenges" with the technology in "many" places that had forced polling officials to suspend the process.
INEC information commissioner Chris Yimoga said he could not give a figure on how many people were affected, with voters also reporting the late and even non-arrival of election officials.
"The problems are not in all the states of the country but in a few states and each of these (resident electoral commissioners) have been informed."
"This is very sad indeed," Peter Ogbuoni, a 31-year-old civil servant, said of Jonathan's problems as he waited to vote in Otuoke in the oil-producing southern Delta.
"If the president could spend more than 30 minutes without being accredited, I wonder how INEC will claim to have conducted a credible election?"
The Boko Haram threat has dominated the election campaign, with the Islamist militant group's leader Abubakar Shekau having threatened to disrupt the vote.
A spate of suicide bombings and attacks on "soft" targets such as markets and bus station raised fears about the safety of voters and led to stringent security measures to be put in place countrywide.
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