An underground complex of stairways, corridors, tunnels and rooms in two storeys, exists beneath the palaces, all along the river side originally, it extended from the Baoli (step-well) near Bengali-Burj to the Machchhi- Bhawan and had entrances from the Baoli, eastern court of Jehangiri-Mahal, Anguri-Bagh and Muthamman-Burj. In fact Akbar built his palace, which originally covered this area, on the existing structures which were converted and used to serve as its foundational basement with which every quarter of his palace was secretly connected. This is also how it assumed such a gigantic height from the river it housed his Harem (seraglio) which had 5000 women including maids. As Historian Abul Fazal recorded, and: notwithstanding the great number of faithful guards but his own vigilance, through this complex. All entrances as also the original stairways, tunnels and corridor have been closed up from time-to-time, and it can now be accessible on by this window.

An octagonal room in its first floor had a Phansighar (Execution-Chamber) with 18.5 feet 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 all along the Fort wall. There is also a Jharokha. 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 treasures in gold, silver coins and jewellery. These underground apartments have now been closed for security reasons. They remain as great amystery today as they were during the Mughal times.