"Two buses were apparently set on fire but we are looking into all possibilities," police spokeswoman Luba Samri told Agence France-Presse.
The incident took place just hours after Israel began running separate bus lines for Palestinian workers and Jewish settlers in the Arab-Israeli town of Kfar Qassem.
Police sources told Israeli army radio that the buses had been torched as a protest against the new transportation system.
The system, which only came into effect on Monday, has sparked claims of segregation.