A statement by Netanyahu's office did not specify the reason for the planned attacks.
However an Israeli military official said Hamas violated the ceasefire by carrying out an attack against Israeli forces in an area under Israeli control.
"This is yet another blatant violation of the ceasefire," the official said.
Netanyahu earlier accused Hamas of violating the agreement by turning over the wrong remains in a process of returning the bodies of hostages to Israel.
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.
The order from Netanyahu follows heightened tensions as Israel reported Hamas firing on its forces in the south of the enclave and after Hamas returned a set of remains that Israel said belonged to a hostage recovered earlier in the war.
Netanyahu called the return a "clear violation" of the ceasefire agreement, which requires Hamas to return all Israeli hostage remains as soon as possible.
Israeli troops were shot at in the southern city of Rafah on Tuesday and returned fire, according to an Israeli military official who spoke on condition of anonymity because there has not been an official announcement yet.
There are still 13 bodies of hostages in the Gaza Strip.
Hamas also 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.
The slow return of hostages' bodies is posing a challenge to implementing the next stages of the ceasefire which will address even knottier issues, such as the disarmament of Hamas, the deployment of an international security force in the Gaza Strip and deciding who will govern the territory.
Hamas has said it is struggling to locate the bodies amid the vast destruction in the enclave while Israel has accused the militant group of purposely delaying their return.
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
