Israel is keeping a prominent Palestinian academic behind bars despite his successful appeal against detention, a Palestinian NGO said on Sunday.

Al-Quds University astrophysics professor Imad Barghouti, 52, was arrested in April and imprisoned without trial for an initial three months, under an Israeli procedure known as administrative detention.

He is accused of inciting violence against Israel, and Israeli media say he is suspected of ties to the militant group Hamas. Barghouti was previously detained while trying to cross into Jordan in December 2014 on unknown charges and set free in January 2015.

The Ramallah-based Palestinian Prisoners Club appealed to an Israeli military court to order his release and at a session on Thursday the court ruled that he should be freed on Sunday.

But the military authorities have now asked for him to be kept in Ofer prison, between Jerusalem and Ramallah.

"The [Israeli] occupation prosecutor today accused prisoner Barghouti of incitement to violence and called for his continued detention after a meeting of the intelligence services," a spokesperson for the club said.

Club lawyer Jawad Boulos said it was a "totally absurd" turnaround.

"The prosecutor said on Thursday after examining the dossier that it would not be possible to file charges because of lack of evidence," Boulos said.

The Israeli army had no immediate comment.

Bargouhti told the US-based Nature Journal that his first detention was over his opposition to the Israeli occupation and for wearing the green scarf and hat of Hamas in his Facebook profile. He denied being a member of the organisation, according to the Times of Israel website.

YouTube videos of Barghouti speaking at Hamas rallies show he was not just a critic of Israeli policy in the West Bank, but was also a vocal supporter of Hamas’s military wing, the Times of Israel also reported.

Barghouthi earned his doctorate at Utah State University in the US, and worked in Jordan and Saudi Arabia prior to accepting a position at Al-Quds University in East Jerusalem in 2000.

Administrative detention allows Israel to hold prisoners without trial for renewable periods of up to six months each.

About 7,000 Palestinians are in Israeli prisons, more than one in 10 in administrative detention.