A third Palestinian militant from the faction Islamic Jihad faction was also killed while preparing a rocket attack, hours after an Israeli civilian was seriously injured when a makeshift missile slammed into his home.
The new bloodshed came as Israel tried to contain the reprisals from the death of eight Palestinian civilians in an explosion on a beach in the northern Gaza Strip on Friday - an incident that prompted Hamas to end an 18-month truce.
The ruling Islamists are also fighting Palestinian president Mahmud Abbas's referendum on coexistence with Israel.
Mr Abbas, a moderate from the formerly dominant Fatah faction, announced on Saturday a first-ever Palestinian referendum to be held on July 26.
The move prompted accusations from Hamas he was engineering a coup against its government, formed after a landslide election win in January.
Voters are being asked to approve calls for an independent Palestinian state on land conquered in 1967, the creation of a national unity government and an end to attacks within Israel.
Hamas attacks
However the prospect of Hamas ending attacks seemed remote after its armed wing claiming to have fired nine missiles into southern Israel.
The attack came even before two of its fighters were killed in an air raid in northern Gaza and another targeted a Hamas vehicle in Gaza City, wounding three people.
"This is a continuation of the Zionist war against our people," Hamas interior minister Said Siam told AFP. "This is an attempt to force the Palestinian people to surrender but this will never happen."
Islamic Jihad, Hamas and a violent Fatah offshoot, the Al-Aqsa Martyrs' Brigades, all claimed responsibility for a series of early morning rocket attacks on southern Israel.
One landed on a house in the town of Sderot, which is home to Defence Minister Amir Peretz, leaving the owner seriously injured.
Amid the background of rising violence, Abbas sought to placate Hamas over his referendum plan by lining up a meeting on Saturday night with Hamas prime minister Ismail Haniya.
A first round of talks between the pair, which dragged on into the early hours, failed to make any headway.
"We failed to agree on the referendum question and we stressed to the president the dangers of this consultation for Palestinian unity," Mr Haniya told reporters after the meeting.
Mr Abbas headed to the Islamists' Gaza stronghold immediately after announcing the referendum at his West Bank headquarters, insisting that the people should have their say on a document drawn up by prisoners held by Israel.
Hamas is furious that the president, who was himself directly elected last year, is trying to bypass its administration.
President “stuck to his guns”
Mr Abbas's spokesman said the president had stuck to his guns in his meeting with Mr Haniya.
"Abu Mazen confirmed to prime minister Haniya that the referendum will be held on the date which has been set but talks will continue," Nabil Abu Rudeina said.
"Dialogue is very important in order that we can arrive at a national consensus to confront the big crisis facing the Palestinian people."
However the prospects of a clear-the-air meeting between Abbas and Hamas's Damascus-based supremo Khaled Meshaal appeared to have been dashed by the president's announcement.
Sources close to both sides said that a furious Mr Meshaal had declared he saw "no need" for such a meeting given Mr Abbas's decision to hold the plebiscite.
Mr Abbas has been at the forefront of the condemnation of the beach killings which seriously embarrassed Israeli Prime Minister Ehud Olmert as he embarked on his first trip to Europe.
Speaking at an Israeli cabinet meeting ahead of his departure to London, Mr Olmert voiced regret for "the death of innocent civilians" and promised that the results of an inquiry would be made public.
But he also promised to "deal" with Hamas, saying it had been involved in attacks for some time.
"We note this and the statements that Hamas commanders have made recently and we will know when and how to deal with it," he added.