The Palestinian Prisoners Club (PPC) on Tuesday reported that PIJ detainees were being segregated and held in "cruel" circumstances in the Ashkelon, Al-Jalama, and other prisons, according to Al-Araby Al-Jadeed.
They are also being taken out to the prison yard with their hands and legs shackled, and fined, the detainee organisation claimed.
All but one of the six Palestinian detainees who escaped Israel's high-security Gilboa Prison by tunneling out earlier this month were part of the PIJ.
The violations come as five detainees are set to be officially accused of assisting the jailbreakers, The Times of Israel reported on Wednesday.
Israel launched a variety of measures, particularly against PIJ detainees, following the 6 September breakout, in an effort to disrupt their organisational apparatus, The New Arab's Arabic sister service, Al-Araby Al-Jadeed, reported.
Meanwhile, in the Naqab (Negev) prison, detainees are being kept in burned-out rooms and denied their basic needs and possessions. Mattresses are given out in the middle of the night, only to be taken away again at 6am, according to the PPC.
The group also said that prisoners are also being placed in waiting rooms and left in cuffs for hours.
PIJ detainees are still fighting against jail authorities by non-compliance with prison rules and engaging in sit-in protests in the jail yards.
Meanwhile, Israel's Shabak domestic intelligence agency and police force revealed they have concluded their inquiry into the Gilboa escape, The Times of Israel reported.
In Nazareth, Israeli prosecutors notified the court on Wednesday that they plan to charge 11 detainees - the six jailbreakers, plus five accused of assisting them.
This is the initial stage in the process of officially bringing accusations against them.
On the same day, Israel police revealed: "As part of the investigation, five inmates from Gilboa Prison were suspected of cooperating and helping the six prisoners escape."
"Operation Freedom Tunnel", as the Gilboa Prison escape is often called in Palestine, was a massive embarrassment for Israel due to the major security lapse. Palestinians held celebrations, heralding the six men as national heroes.