Hamas sources claimed that two of those killed in Sunday night's attack were from the Palestinian resistance group's military wing, Izz al-Din al-Qassam.
An unidentified eye-witness told Reuters the men were walking near a beach in the heart of Gaza City when the missiles struck.
"The four men were sitting on a hilltop overlooking the beach," he said. "They stood up and were about to cross the road when helicopters fired four missiles."
The two dead Hamas members were Wahid al-Hams and Ahmad Shtawi.
The missile attack beheaded some of the men and burned their bodies beyond recognition, medics said.
Israeli army chief Moshe Yaalon had warned earlier that his forces would hunt down Hamas leaders if Palestinian security forces failed to reign them in.
Several other people were wounded in the incident, which took place close to the local offices of the Palestinian leader Yasir Arafat.
The injured were taken to the city's main al-Shifa hospital.
Israel assassinated a senior Hamas leader in a similar missile strike in the Gaza Strip on Thursday to avenge the resistance bombing of a bus in Jerusalem.
Sunday's helicopter attack came shortly after Arafat's chief of security in Gaza ordered a halt to rocket and mortar strikes on Israelis, security sources said.
A statement issued by Major-General Abd al-Razek al-Majaydeh on Sunday said forces under his command had been instructed to "maintain security and stability in all border areas and ... to prevent violations".
Palestians launched deepest ever rocket attack into Israel.
The Israeli army statement was made just hours after Palestinian fighters carried out their deepest ever rocket strike, landing a Qassam-2 rocket close to a lifeguard station on Zikim beach, near the Israeli coastal city of Ashkelon.
Arafat's appeal to end attacks on Israel suggests he has yielded to US pleas to lean on Palestinian security forces to help reformist Prime Minister Mahmud Abbas curb resistance groups.
Arafat may also have been responding to suggestions that he will be expelled from the Palestinian Territories if there was another big resistance attack.
Israeli Army Radio on Sunday quoted sources in Jerusalem saying that "Yasir Arafat will be expelled from the territories after the next big terror attack."
The sources said that although a final decision has not yet been made on the matter, another large-scale attack would compel Israel to expel Arafat.
Relations between the Palestinian president and unelected PM remain mercurial at best.
Palestinian officials said tensions flared between the two earlier on Sunday over a proposal, aired in the Fatah central committee, to name Nasir Yusuf as interior minister.
"This decision (to propose Nasir Yusuf) is not a correct decision," Abbas's office said in a brief statement conveyed to AFP.
Yusuf is a general with ties to Arafat. Abbas is currently resonsible for the Interior Ministry.
Arguments over the control of different security services has hampered efforts to reign in fighters.
Arafat has come under heavy US pressure to hand over complete control of the security apparatus to Abbas and his security chief Muhammad Dahlan so they can crack down on hardline Palestinian groups.
Abbas rejected the idea of a new interior minister and reiterated his demand that Arafat cede all his remaining security responsibilities.
The Fatah proposal serves to highlight continued discomfort among Arafat supporters with Abbas.
Abbas was named Prime Minsiter in April with the blessing of the US government, seeking to push its "road map" for peace.
Still, efforts his efforts to curb resistance groups have been stymied by Palestinian infighting and the continuing round of violence on that wrecked a truce proclaimed by the groups on 29 June.
Abbas controls three of the many Palestinian security branches: the civil police, civil defence and preventative security force.
The 35,000-40,000 strong national security force and other branches such as intelligence, the navy and border police are still under Arafat's command.
A Palestinian security source, who asked not to be named, said more action would follow. "The Palestinian government will implement law and order. We'll go after everybody," he said.