Israeli army officials said the strike Wednesday targeted operatives of the Hamas affiliate Defenders of al-Aqsa who allegedly were planning a terror attack against Israel, Ynetnews.com reported.
The critically injured man was hospitalized in Rafah, near where the airstrike occurred.
Hamas officials said the two deceased men worked as the security forces of the Hamas government in Gaza, the Palestinian news agency Ma'an said.
The Interior Ministry said the two deceased were on official business concerning securing the Gaza-Egypt border.
The ministry said the airstrike was an indication that Israel planned to initiate wide-scale operations in Gaza, Ma'an said.
The Israeli military said in a statement, Israel "will not tolerate any attempt by terrorist groups to harm" Israeli civilians and soldiers and would "operate with strength and determination against those who use terror against the state of Israel."