Both the Palestinian Authority and the Higher Arab Monitoring Committee called for strikes, Ynetnews.com reported.
In a speech, Palestinian Authority President Mahmoud Abbas said, "We will remain on our land … like our olive trees."
For the Palestinians Nakba Day is an annual commemoration of the displacement that followed the Israeli Declaration of Independence in 1948.
The Israeli military was on high alert and augmented its presence in West Bank cities and along the Gaza border ahead of possible clashes.
Several arrests were reported in cities across the West Bank, the Palestinian Ma'an News Agency said.
Palestinians clashed with Israeli soldiers at the Qalandiya checkpoint in the West Bank, Ynetnews.com said. Dozens of Palestinians also rioted and burned tires at a checkpoint near the Cave of the Patriarch, officials said.
High Arab Monitoring Committee Chairman Mohammad Zeidan urged Nakba Day participants and security forces to avoid confrontations with Israeli security forces.
"I hope today will be uneventful. I ask the Arab people to respect the strike, the Nakba and the security prisoners," Zeidan said. "I also urge the [Israeli] police to stay away from the rallies. The situation is sensitive and we don't want to see any clashes."
Observers said hundreds of demonstrators gathered at an Israeli jail near Ramallah on the West Bank, where security forces lobbed tear gas at the protests, Ma'an said.
Israeli activists confronted Arabs and their sympathizers on Israeli campuses Tuesday for the second straight day, Arutz Sheva reported. Arabs at the Har Hatzofim campus of Hebrew University waved Palestine Liberation Organization flags and chanted PLO slogans.
The PLO's research center released its annual census of Palestinians, reporting there were 11.2 million Palestinians worldwide.