At least 13 people were killed in the strikes, including six women and four children, the Director of Al-Shifa Medical Complex, Muhammad Abu Salmiya, said Tuesday.
Earlier, the Ministry of Health in Gaza said 20 people had been injured and warned the number of casualties could rise.
“Ambulance crews are still continuing to evacuate victims from the areas targeted by the occupation,” the Ministry of Health said, referring to Israel.
The Israel Defense Forces (IDF) confirmed it launched pre-dawn airstrikes on Gaza, saying it was a “response to incessant aggression on the part of the Islamic Jihad terrorist organization.”
IDF spokesman Lt. Col. Richard Hecht called the targets “kingpin terrorists” and insisted that the military “did as much as we could to focus on them.”
But he also conceded the IDF was “aware of some collateral,” an apparent reference to the wives and children who were also killed alongside those being targeted.
“If there were some tragic deaths, we’ll look into it and get back to you,” he said in response to reporters’ questions.
Palestinian militant group Islamic Jihad confirmed three of its commanders were killed in the operation along with their wives and children.
The Al Shifa hospital in Gaza said those killed were members of four families plus one other individual.
The commanders killed were Jihad Shaker Al-Ghannam, secretary of the Military Council in the al Quds Brigades; Khalil Salah al Bahtini, commander of the Northern Region in the al Quds Brigades; and Tariq Muhammad Ezzedine, one of the leaders of the military wing of the al Quds Brigades in the West Bank, the group said.
Islamic Jihad said Ghannam, 62, was also commander-in-chief of the al Quds Brigades and has been wanted for over 20 years, having survived five previous assassination attempts.
He had worked in Yasser Arafat’s Fatah and the Popular Resistance Committees, secular Palestinian militant groups that predate the emergence of Palestinian Islamic Jihad, the group said.
The IDF accused Ghannam of coordinating weapons and money transfers between Islamic Jihad and Hamas, the militant group which runs Gaza. It called him one of the most senior members of Islamic Jihad.
Calling the strikes “Operation Shield and Arrow,” the IDF said its fighter jets and helicopters hit 10 Islamic Jihad targets, including what it said were “rocket production workshops in Khan Yunis,” weapon manufacturing sites, military compounds, a concrete manufacturing site and a military post in southern Gaza.
Video from Gaza showed explosions lighting up the night sky and the rubble from buildings hit by the strikes.
The latest violence came almost a week after Israel and Palestinian militants in Gaza exchanged fire following the death of a prominent Palestinian hunger striker in an Israeli prison.
Israel conducted strikes on what it said were targets belonging to Hamas as dozens of rockets were fired from Gaza toward Israel on May 2.
It followed the death of Palestinian detainee Khader Adnan, an Islamic Jihad former spokesman who became a symbol of Palestinian resistance to Israeli detention policies, in Israeli custody after 87 days of hunger strike.
IDF spokesman Hecht said planning for Tuesday’s operation began after the rocket fire from Gaza last week.
The strikes took place overnight Monday because of a convergence of intelligence information, weather and permissions, he said, adding some 40 IDF aircraft were involved in the operation.
Gaza is one of the most densely packed places in the world, an isolated coastal enclave of almost two million people crammed into 140 square miles.
Governed by the Palestinian militant group Hamas, the territory is largely cut off from the rest of the world by an Israeli blockade of Gaza’s land, air and sea dating back to 2007. Egypt controls Gaza’s southern border crossing, Rafah.
Israel has placed heavy restrictions on the freedom of civilian movement and controls the importation of basic goods into the narrow coastal strip.
Hecht said he did not know if there would be more follow up strikes.
“We don’t know yet where we go. It’s still early,” he said. “We’re ready for as long as it takes. The big question is Hamas. What will they decide to do?”
CNN’s Ibrahim Dahman reported from Gaza and CNN’s Abeer Salman and Richard Allen Greene reported from Jerusalem.
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