An underground complex of stairways, corridors, tunnels and chambers exist beneath the palaces all along the riverside. Originally it extended from the baoli (step-well) near Bengali burj to the Macchi Bhawan and had entrances from the baoli, eastern court to Jahangiri Mahal, Anguri Bagh and Musamman Burj. In fact Akbars palace, which was originally converted and used to serve as its foundational basement with which every quarter of his palace was secretly connected. Such a gigantic height from the river, it housed his harem (seraglio) which had 5000 women. Abdul Fazl records that not withstanding the great number of faithful guards, Akbar kept his own vigilance through this complex. All entrances as also the original stairways, tunnels and corridors have been closed and are now accessible only through a window.
It is believed that an octagonal room in its first floor had a Phansighar (execution chamber) with 5.7 m. long wooden beam across it for private execution of offenders of the harem chastity. Babur's baoli and well, a tank with cascade and series of rooms are also there. Slits for ventilation are given in the corridor which runs along the Fort wall. There is also a Jharokha in the second floor below. It is more spacious and has larger apartments and a more complex network of halls, rooms and corridors. Agra Fort contained the largest treasury of the Mughal Empire and this floor was probably reserved for storing treasure in gold, silver, coins and jewellery. These underground chambers have now been closed for security reasons. They remain a great mystery even today as they were during the Mughal times.