The operation also left two members of the Hamas security forces dead.
The main suspect in a recent bomb attack against the Palestinian prime minister in the Gaza Strip was killed in an arrest raid on Thursday that also left two members of the Hamas security forces dead.
One of the suspect's alleged accomplices was also killed in the raid after Hamas – which governs the Gaza Strip - launched a manhunt.
The interior ministry in the Gaza Strip announced the deaths. The two suspects were earlier said to have been arrested, but the ministry issued a statement later saying they had died from their wounds.
A third suspect was under arrest.
The members of the security forces were named as Hammad Abu Swerah and Ziad al Howajri, with the interior ministry saying they "died while carrying out their national duty in a security operation this morning."
A clash with an exchange of fire had erupted earlier in the day in Nuseirat, south of Gaza City, a day after Hamas named Anas Abu Koussa, born in 1993, as the lead suspect.
Dozens of new checkpoints had been erected throughout the Palestinian enclave and armed security forces were searching cars.
Attack on PM Rami Hamdallah
Palestinian Prime Minister Rami Hamdallah was unhurt by the roadside bomb that struck his convoy on March 13, in what Palestinian officials have called an assassination attempt as he entered Gaza on a rare visit.
The roadside bomb, believed to have weighed around 15 kilos, exploded a few hundred metres from the border with Israel, shortly after Hamdallah's convoy entered the territory.
A second bomb failed to explode, officials said.
Hamas did not give a possible motive for the attack on Hamdallah, head of government in President Mahmoud Abbas' Palestinian Authority (PA).
On Wednesday, a Hamas security source said investigators had arrested and were questioning three people, including two members of the PA-run intelligence services.
Reconciliation efforts hit
On Monday, Abbas accused Hamas of being behind the blast and said he would take new measures in response, without specifying details.
Hamas and the West Bank-based PA have been bitter rivals for a decade since Hamas seized control of Gaza and won fair elections in the blockaded enclave.
The bombing appears to have brought to an end hopes for an already floundering reconciliation deal signed in October between Hamas and Abbas' Fatah party, which dominates the PA.