The fire at the offices of B'Tselem, an Israeli group that monitors human rights among Palestinians, took place at a time of heightened tensions. Scores of people have been killed in several months of violence in Israel and the occupied West Bank.
Firefighters arrived at the offices, in a quiet Jerusalem neighbourhood, and extinguished the blaze. There were no reports of casualties, police spokeswoman Luba Samri said.
Now in its fourth month, the wave of bloodshed has raised fears of wider escalation, a decade after the last Palestinian uprising subsided. Palestinian stabbings, car-rammings and shooting attacks have killed 21 Israelis and a US citizen.
Since October 1 Israeli forces or armed civilians have killed at least 139 Palestinians, 89 of whom authorities described as assailants. Most others have been killed in clashes with security forces.
Vandalism attacks, including torchings, by suspected far-right Israeli groups have caused damage to Palestinian property and mosques and churches.
Two Israelis were charged last week over the death of a Palestinian baby and his parents in the West Bank last year after their home was set on fire.
Israel's right-wing government has proposed legislation to limit foreign donations from governments and private benefactors to B'Tselem and many other Israeli NGOs, something that could severely restrict their ability to operate.