No injuries were reported from the explosions on Thursday, which happened while Israel was already grieving after Hamas returned the bodies of four hostages from Gaza.
The bus explosions were reminiscent of bombings during the Palestinian uprising of the 2000s, but such attacks are now rare.
Police spokesman Asi Aharoni told Channel 13 TV that explosives were found on two other buses.
Israeli police said the five bombs were identical and equipped with timers, and said bomb squads were defusing the unexploded bombs.
Bomb disposal units had finished searching buses and trains nationwide for additional bombs and police were on the scene Bat Yam, a city outside Tel Aviv, as they searched for suspects.
"We need to determine if a single suspect placed explosives on a number of buses, or if there were multiple suspects," police spokesman Haim Sargrof told Israeli TV.
Tzvika Brot, mayor of Bat Yam, said it was a miracle no one was hurt.
The empty buses had finished their routes and were in a parking lot, he said.
The Shin Bet internal security agency was taking over the investigation, police said, and Israeli Prime Minister Benjamin Netanyahu's office said he was receiving updates from his military secretary and following the events.
Sargrof said the explosives matched explosives used in the West Bank, but he declined to elaborate.
Israel has repeatedly carried out military raids on suspected Palestinian militants in the West Bank since Hamas's October 7, 2023, attack sparked the devastating war in Gaza.
As part of that crackdown, it has greatly restricted entry into Israel for Palestinians from the occupied territory.
A group identifying itself as a branch of Hamas' military wing, Qassam Brigades, from the northern West Bank city of Tulkarem, posted on messaging app Telegram: "We will never forget to take vengeance for our martyrs as long as the occupation is on our lands."
The city of Tulkarem and two refugee camps in the city have been a focus of recent Israeli army raids.
Since the ceasefire with Hamas in Gaza took effect on January 19, Israel has been conducting a broad military offensive in the West Bank.
Brot, the mayor, urged the public to keep their routines, saying schools would be open on Friday and public transport would operate.
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