The brutal killing on July 2 has triggered four days of violent clashes which began in east Jerusalem and have since spread to more than half a dozen Arab towns in Israel, with hordes of angry protesters hurling stones at Israeli riot police.
"Apparently the people arrested in relation to the case belong to an extremist Jewish group," an official said, speaking on condition of anonymity.
The website of Haaretz newspaper said six people had been arrested, but details of the case have been subjected to a strict gag order.
It followed days of growing suspicion that Wednesday's murder was carried out by extremist Jews in revenge for last month's abduction and murder of three Israeli teenagers in the occupied West Bank.
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Tensions continued to rise in the south with Gaza militants firing another nine rockets over the border, despite a night of 10 air strikes.
But Israel appeared bent on containing the situation, with Prime Minister Benjamin Netanyahu urging his cabinet to keep a cool head over how to handle growing tensions in and around Gaza.
The violence exploded as a top Palestinian legal official confirmed that initial findings from the post mortem showed there was smoke in the lungs of 16-year-old Mohammed Abu Khder, indicating he was still alive when he was set on fire.
The grisly murder has sparked shock, disgust and an outpouring of condemnation from both Israeli and Palestinian leaders.
But until today, police said they were unsure of the motive for the killing, contributing to the rising tensions.
"Around 35 people were arrested overnight, almost half of them minors," police spokeswoman Luba Samri said after violence raged into the early hours today.
The rest were arrested in the so-called Triangle, a concentration of Arab towns and villages close to the northwestern sector of the Green Line -- Taibe, Tira, Qalansuwa, Jaljulia and Umm el-Fahm.
"We are demonstrating against this incitement to hatred by Israelis online, who are saying 'death to Arabs'," one demonstrator in Qalansuwa told army radio.