The Palestinian Popular Resistance Committees accused Israel of trying to kill its fighters in a strike on their car on Sunday.
The Israeli army said it carried out an air strike on three armed men several metres from a fence near the Karni border crossing in northern Gaza, believing that they were trying to penetrate the fence. They army said it hit one fighter.
Palestinian witnesses said there was a small crater and what looked like pieces of a missile near the car. They said Israeli helicopters were hovering over the area - near to where the
army acknowledged opening fire.
The Palestinian Popular Resistance Committees said its fighters had been travelling in the car but escaped the explosion.
A spokesman for the group said a bystander was killed. Dr Moaiya Hassanain, a Palestinian hospital official, identified the dead man as a Mohammed Abdel-Al, 22, of Gaza City.
The Popular Resistance Committees vowed retaliation.
"The Popular Resistance Committee has the right to respond to the crime of assassination," said Abu Yousef, a spokesman for the group.