"We have received the bodies of three soldiers and seven more wounded," said Khalil Gouider, spokesman for the Benghazi Medical Centre.
Security services spokesman Ibrahim al-Charaa said an army convoy en route to provide security for a polling station in the southern district of Al-Houari had been attacked by the Rafallah al-Sahati Islamist group.
In contrast, the group said on its Facebook page that the convoy had withdrawn after "provoking" its fighters and that there had been no casualties.
Both Haftar, who launched an anti-Islamist campaign last month that has taken hundreds of lives, and his foes had said they would observe a truce during the election.
Officials said the violence did not interrupt voting in the flashpoint city, cradle of the 2011 uprising that ousted and killed long-time dictator Moamer Kadhafi.