A meeting between Shia cleric Kalb-e-Jawwad and the chief minister took place late Wednesday in which the issue was discussed.
Sources said the Shia community is divided over the appointments, alleging that Azam Khan was bribed for them.
"The people being appointed to the board are corrupt and would lead to large scale malpractises," Kalb-e-Jawwad told IANS.
He sought an immediate and convincing response from the state government on the matter and said he has given a five-point charter of demands to the chief minister. One of its demands is to take the Waqf department out of Khan's control.
He also said he has been assured that "no injustice" will be done.
Violence had erupted in the city when a Shia protest march proceeding towards the minister's house was intercepted by police. In the clashes later, one person was killed and many were injured, leading to tensions on the day of Alvida Namaaz - the last Friday of the holy month of Ramadan.