Hamas Parliament President Aziz Dwaik was arrested on Thursday at the Jaba checkpoint near Ramallah, while on his way to Hebron.
The Palestinian Parliament released a statement denouncing the arrest and appealing to Egypt to intervene for his immediate release.
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The IDF confirmed that Dwaik was detained for suspected terror activity.
Palestinian sources said that when Dwaik's car arrived at the checkpoint he was stopped, handcuffed and blindfolded, before he was taken to an undisclosed location.
A second person traveling with him was detained as well, but was later released.
Aziz Dwaik during his trial in Israel (Archives: AP)
Deputy Speaker of Hamas Parliament Ahmad Bahr urged Egypt and the Arab League to facilitate Dwaik's release.
Hamas government spokesmen Taher Nounou denounced the arrest, saying Israel was attempting to sabotage the work of the Palestinian parliament.
Dwaik was arrested in 2006, as part of a series of arrests made by the IDF following the abduction of Gilad Shalit .In 2008 he was convicted of affiliation with a terror organization and was sentenced to three years in prison. He was released in 2009.
Yoav Zitun contributed to this report