An Israeli army spokesman said that troops operating in the area shot and killed three armed Palestinians in an exchange of fire. He did not know of a fourth man killed.
Witnesses, however, said the four men were standing on a street in the Shijaiya district of Gaza City when a missile hit them on Monday.
Aljazeera said five Palestinians, including four members of the interior ministry's paramilitary force, were killed in the Israeli air strike.
The deaths bring the total number of Palestinians killed by Israelis in Shijaiya to eight, including three who were killed on Sunday.
Another 18 Palestinians, including two journalists, have been injured in the Israeli operation.
The Israeli army said its operation in the neighbourhood was aimed at seeking out tunnels and explosives that could be used in attacks.
Wail al-Dahduh, Aljazeera's correspondent in Gaza, said an Israeli reconnaissance plane fired at least one missile at a group of paramilitary force personnel. The direct hit killed all four members of the group.
The men had been deployed at a crossroads near the eastern part of Shijaiya, which has been the scene of a major military operation by Israeli forces.
Palestinian medical sources said the bodies of the four had been burned and torn to shreds by the impact of the missile.
A fifth Palestinian was killed in a house nearby, al-Dahduh said, adding that his body too was barely recognisable.
Meanwhile, Israeli Apache helicopters and reconnaissance planes are policing the skies, occasionally opening fire, he said.
The Israeli operation in Shijaiya has entered its second consecutive day, with tanks regularly opening fire on Palestinian homes, al-Dahduh reported.
More than 180 Palestinians have been killed since Israel launched an offensive in June aimed at recovering a captured soldier and ending cross-border rocket fire.