Deputy Director Jatan Kumar Roy filed the cases filed at Motijheel Police Station at 5pm on Tuesday, ACC spokesperson Pranab Kumar Bhattacharya told bdnews24.com.
He said the move had been approved at a meeting earlier in the day.
The anti-graft watchdog has found evidence of the secretary misusing his power to obtain RAJUK plots for himself and the members of his family.
It began investigating the allegations against Hossain on Feb 5.

The probe, by Jatan Kumar Roy, lasted nearly one and a half months.
The secretary is said to have unlawfully increased the area of a plot, seven kathas, allotted to his wife in RAJUK’s Purbachal housing project to 12 kathas in two phases.
He is believed to have also used his influence to similarly increase the area of plots he bought for himself and his mother at the Uttara Apartment Project from three kathas to five kathas.
Bhattacharya said gross irregularities and misuse of power had been detected in the allotment of the three plots. The aberrations, he said, were punishable under the anti-corruption law.
A BCS cadre of the 1982, Hossain is currently the secretary of the expatriate welfare ministry. He was the secretary to the housing and public works ministry during the previous Grand Alliance government.
At that time, Abdul Manna Khan was the state minister for public works. He is among the several MPs and ministers of that government who are currently facing ACC investigation over an unaccounted growth in their assets.