The Prisons Service said in a statement the prisoners resisted at Shikma prison in the Mediterranean city of Ashkelon after guards tried to search a cell following the discovery of a sketched map of the jail on a prisoner.
Palestinian officials confirmed the riot began after a search and said it was not connected with Palestinian demands for Israel to free prisoners in efforts to boost US-led peace moves.
"They are rioting and police have been called to assist," a police spokesman said.
Riot sparked by hidden map
Witnesses said dozens of police cars and ambulances were parked outside the prison, but it was not immediately clear if there were any casualties or whether the situation was back under control.
The prisoners began banging on their doors and threw sharp objects and burning papers."
-Israeli Prison Service statement
"Following the discovery of a slip of paper hidden on a security prisoner from Shikma prison, with a sketch of Shikma prison on it, it was decided to search his cells as well as the cells of other inmates in the prison," the Prison Service said.
"The prisoners vigorously resisted the entry of guards... The prisoners began banging on their doors and threw sharp objects and burning papers."
Palestinian demands for Israel to free all Palestinian prisoners are key to the US-led peace efforts after 34 months of Israeli-Palestinian conflict. Israel has freed some prisoners but the Palestinians say all 6,000 must be released.