Awad Rajub, 29, was whisked away from his home in Dura, near the West Bank city of Hebron, on Tuesday.
An Israeli army spokesman said Rajub was still in detention.
Sources told Aljazeera that Rajub, a Palestinian, was beaten up in the presence of his wife by the Israeli soldiers. His computer and mobile phone were also confiscated.
Rajub was later taken to an undisclosed location.
Walid al-Amari, Aljazeera's bureau chief for Jerusalem and the Palestinian territories, said: "The army simply said that he had been arrested for security reasons, and we do not know any more than that."
Israeli public radio said Rajub was arrested after the army received information about him from the domestic Israeli security service, Shin Beth.