Palestinian groups admit using ceasefire to train and better arm themselves.
More than 11,000 Palestinians are held in Israeli prisons, many of them detained for long periods without trial.
Nour Odeh, Al Jazeera’s correspodent reporting from Ramallah, said: “Palestinian detainees inside the miltary camp tried to prevent Israeli prison authorities from raiding their sections and undertaking a search of the wards.
“We have heard repeatedly from these detainees about the humiliation they undergo on a daily basis during these searches.
“And it was at this point they [inmates] wanted to protest against the measures undertaken by the Israeli prison authorities.”
She said that calm appears to have been restored and situation brought under control. But it is unclear whether the Israeli authorities will respond to the Palestinian prisoners’ frustrations and grievances after the latest incident.
In the Gaza Strip, meanwhile, a Palestinian man has been killed in an Israeli missile attack – the first death since the end of a six-month-old ceasefire between Israel and Hamas, which controls the Palestinian territory.
Ali Hijazi, 22, and two other men who were wounded in Saturday’s incident were members of the al-Aqsa Martyrs Brigades, witnesses said.
The air raid targeted a group of fighters firing rockets towards Israel, an Israeli military official said.
The attack in Beit Lahiya in the northern Gaza Strip came a day after the end of the ceasefire.
Sherine Tadros, Al Jazeera’s correspondent in Gaza, said: “The [Israeli] military told us that six projectiles have been launched from the Gaza Strip towards southern Israel.
“This is coming as very sad news for the people here who once again find themselves in the position they were in before the ceasefire, in terms of this almost daily aggression by Israel and very uncertain times in terms of what will happen next.
“From the Israeli side they have said that … as long as there is peace from the Palestinian side they will respond with peace. But if there is aggression by Palestinian factions, they will fight back with force.”
A ceasefire agreed in June officially ended at daybreak on Friday, after Hamas said it would not renew it.
Hamas blamed Israelis for the failure of the ceasefire, saying that they had not lived up to their obligations under the deal by continuing a blockade of the Gaza Strip.