No casualties were reported in the explosions.
The Israeli police earlier said there had been explosions on three buses in two Israeli suburbs outside Tel Aviv on Thursday and four explosive devices were found.
Local media reported the explosions had occurred on buses in depots and were empty.
The explosions were a stark reminder of the devastating bus bombings in Israel that were a hallmark of the Palestinian uprising of the 2000s, although such attacks are now rare.
The military said it was assisting the police and Shin Bet intelligence agency in the investigation.
The police said it was searching for suspects and advised the public to remain vigilant as other buses were inspected.
There was no immediate claim of responsibility for the explosions.
Netanyahu's office said the prime minister had ordered the military to carry out "an intensive operation against centres of terrorism" in the West Bank.
He had met the defence minister, the heads of the military and security agency Shin Bet, and the police commissioner following the explosions, his office said.
The military said it had blocked entry points in certain areas of the West Bank, without specifying where.
A video published by local media showed what appeared to be a bus on fire at a depot and a photo of a burned-out bus.
The military has been conducting a large-scale military operation in the West Bank in the past month that it says is targeting militants.
Tens of thousands of Palestinians have been forced to leave their homes in refugee camps, while homes and infrastructure have been demolished.
The bus blasts come amid a fragile ceasefire in Gaza between the Palestinian militant group Hamas and Israel after 16 months of war.
Hamas on Thursday released the bodies of four hostages.
The ceasefire has held since it was implemented on January 19 despite accusations traded by Israel and Hamas of violations.
The Israeli transport minister has told the Public Transit Authority that all buses, trains and light-rail trains should be stopped and inspected, Israeli media reported.
