The decision was part of a limited reshuffle in the ministry in charge of security. The minister also replaced the heads of the security and investigative bureaus in the southern governorate of Minya, where there have been attacks on government buildings and churches during weeks of unrest.
A security official said Minister Mohammed Ibrahim removed the head of the prison authority Mostafa Baz, who had been in the post since June 10.
The official said there was no official explanation for the removal. He said the decision comes after reports that Baz had overlooked meetings in jail between Muslim Brotherhood leaders and other Islamists, and allowed them to communicate with people outside the prisons.
Authorities accuse the Brotherhood of organising a campaign to destabilize Egypt. Security officials have arrested hundreds of the group's members in the wake of the July 3 military coup that toppled Islamist President Mohammed Morsi.
Also Read
In an interview with a private television station this week, Baz denied he facilitated meetings between the leadership. He said reports in the media were referring to when several leaders of the group and other Islamists prayed together.
Baz said police officers outnumbered the Islamists at the prayer in an attempt to show that they were monitored.
Baz said he strictly followed prison regulations, dismissing reports that the leaders are allowed contacts with the outside world, apparently through mobile phones smuggled to the prison.