Khader Adnan, who was awaiting trial, was found unconscious in his cell on Tuesday and taken to hospital where he was declared dead after efforts to revive him, Israel's Prisons Service said. He had refused any medical assessments or treatment, it added.
Hundreds of people took to the streets in Gaza to rally in support of Adnan and mourn his death, and the Israeli military said three rockets were fired into Israel from the strip.
Since 2011, Adnan had conducted at least three hunger strikes in protest at detentions without charges by Israel. The tactic has been used by other Palestinian prisoners, sometimes en masse, but none had died since 1992.
Disputing the Prisons Service account, Adnan's lawyer Jamil Al-Khatib and a doctor with a human rights group who recently met him accused Israeli authorities of withholding medical care.
"We demanded he be moved into a civilian hospital where he could be properly followed up (on). Unfortunately, such a demand was met by intransigence and rejection," Al-Khatib told Reuters.
Adnan, 45, was from Jenin in the Israeli-occupied West Bank. Islamic Jihad sources said he was one of its political leaders. The faction has a limited West Bank presence but is the second most powerful armed group in Hamas-ruled Gaza, where Israeli forces fought a brief war against it last August.
Lina Qasem-Hassan of Physicians for Human Rights in Israel said she saw Adnan on April 23, at which point he had lost 40 kilograms and was having trouble breathing but was conscious.
"His death could have been avoided," Qasem Hassan told Reuters, saying several Israeli hospitals had refused to admit Adnan after he made brief visits to their emergency rooms.
The Prisons Service said hospitalisation had not been an option as Adnan had declined "even a preliminary inspection".
"Our fight is continuing and the enemy will realise once again that its crimes will not pass without a response," Islamic Jihad, which preaches Israel's destruction, said in a statement.
Three rockets launched from Gaza toward Israeli border communities fell in open areas but set off sirens which sent residents rushing to shelters, Israel's military said.
Israel said it was cancelling a military drill that had been planned for the Gaza periphery "pursuant to a situational assessment", and was putting staff in security prisons on heightened alert. In the West Bank, Israeli authorities said a man was hurt in a shooting near a Jewish settlement.
There was no immediate claim of responsibility for the Gaza rockets reported by Israel or the West Bank incident.
According to the Palestinian Prisoners Association, Adnan had been arrested by Israel 12 times, spending around eight years in prison, mostly under so-called "administrative detention" - or detention without charges.
Israel says such detentions are required when evidence cannot be revealed in court due to the need to keep intelligence sources secret. Palestinians say they deny due process of law.
This time, Adnan was arrested and indicted in an Israeli military court on charges that included links to an outlawed group and incitement to violence, the Prisons Service said.Â
