Officials from Hamas, which controls the Gaza Strip, confirmed the men were members of Islamic Jihad, who had been on foot close to the fence with Israel.
An Israeli army spokeswoman confirmed an air assault had been carried out.
Israel frequently launches missiles on the Gaza Strip in what it says is an effort to stop armed groups fighting the Israeli occupation from launching rockets into southern Israeli towns and planting bombs along the border that target its soldiers.
Friday's attack brings to 6,151 the number of people killed since the start of the second Palestinian uprising in 2000, the vast majority of them Palestinians, according to an AFP tally.