He was hospitalized with what were called moderate wounds after he returned from Friday prayers in Gaza City, opened his car door and was met with an explosion, the statement said. It added that several bystanders were also injured.
Hamas did not single out any organization for the blast, and none admitted responsibility. Israel's Foreign Ministry offered no comment.
"Whoever was behind the assassination attempt, I am sure that our security forces can find them," said Salama Marouf, head of the Hamas media office in Gaza.
The attack came as Hamas and rival group Fatah attempt to unify their control of Gaza and the West Bank. In September, an Egyptian-brokered agreement was signed to work toward Palestinian elections, but 10 years of mistrust have led to opposition by some within each movement. Israeli officials have also expressed their discomfort with the reconciliation.
Radical groups within Gaza have also denounced the agreement to mutually operate the two territories, west and east of Israel, who have expanded relations with Islamic State affiliates in Egypt's Sinai Peninsula.
Naim is regarded as close to Yahya Sinwar, Hamas leader in Gaza. Both Naim and Sinwar were released by Israel in a 2011 prisoner exchange.