The Israeli strikes targeted an area close to Shifa hospital, the largest operational hospital in northern part of the Gaza Strip, witnesses and Hamas media said.
There was no word yet on any casualties.
The Israeli military did not immediately comment on the strikes, which were the latest violence in a fragile three-week-old ceasefire and which followed a statement by Netanyahu's office saying he had ordered immediate attacks.
The statement did not give a specific reason for the attacks but an Israeli military official said Hamas had violated the ceasefire by carrying out an attack against Israeli forces in an area of the enclave that is under Israeli control.
"This is yet another blatant violation of the ceasefire," the official said.
The US-backed ceasefire agreement went into effect on October 10, halting two years of war that was triggered by deadly Hamas-led attacks on Israel on October 7, 2023 and that has devastated the narrow coastal strip.
Both sides have accused each other of violations.
On Saturday, Israel said its forces carried out a "targeted strike" on a person in the centre of the Gaza Strip who was planning to attack Israeli troops.
Earlier on Tuesday Netanyahu accused Hamas of violating the ceasefire by turning over some wrong remains in a process of returning the bodies of hostages to Israel.
Netanyahu said the remains handed over on Monday belonged to Ofir Tzarfati, an Israeli killed during Hamas' October 7, 2023 attack.
Tzarfati's remains had already been partially retrieved by Israeli troops during the war.
Hamas initially said in response to this that it would hand over to Israel on Tuesday the body of a missing hostage found in a tunnel in the Gaza Strip.
However, Hamas' armed wing, al-Qassam Brigades, said later it would postpone the planned handover, citing what it said were Israel's violations of the ceasefire.
Israeli media earlier reported an exchange of fire between Israeli forces and Hamas fighters in the southern Gaza city of Rafah.
The Israeli military did not respond to a request for comment on the reports.
Hamas said it was complying with the ceasefire terms and Netanyahu was looking for excuses to back away from Israel's obligations.
Under the ceasefire terms, Hamas released all living hostages in return for nearly 2000 Palestinian convicts and wartime detainees, while Israel pulled back its troops and halted its offensive.
Hamas has also agreed to hand over the remains of all dead hostages yet to be recovered but has said that it will take time to locate and retrieve the bodies amid Gaza's ruins.
Israel says the militant group can access the remains of most of the hostages.
The issue has become one of the main sticking points in the ceasefire, which US President Donald Trump says he is watching closely.
US Vice President JD Vance said on Tuesday the ceasefire was holding despite Israeli strikes in Gaza City and both Israel and Hamas accusing each other of violations.
"The ceasefire is holding. That doesn't mean that there aren't going to be little skirmishes here and there," Vance told reporters.
"We know that Hamas or somebody else within Gaza attacked an (Israeli military) soldier. We expect the Israelis are going to respond but I think the president's peace is going to hold despite that."
There are still 13 bodies of hostages in the Gaza Strip.
Hamas said on the Telegram messaging app that any Israeli escalation of attacks would hinder search and recovery operations and delay the return of the bodies of Israeli soldiers.
Over the weekend, Egypt deployed a team of experts and heavy equipment to help search for the bodies of the remaining hostages.
That work continued on Tuesday in Khan Younis and Nuseirat.
with Reuters
