Malik who met with residents of the Lyari area announced that there would be no talks with the banned Peoples Aman Committee and called on all criminals to surrender.
Malik's visit to Lyari came after the government suspended the operation on Friday amidst increasing pressure from the media, opposition parties and civil right bodies that innocent residents were facing hardships and were caught in the gun battles between the police and criminal gangs.
Malik went to Lyari one day after violence was reported from other parts of the city in which at least seven people were killed including the son and grandson of a worker of the ruling Pakistan Peoples Party.
Police said that the attack, described by the PPP as 'targeted killing' was followed by arson attacks that created tension and paralysed the routine life in the whole Kati Pahari area.
Malik said police would only carry out targeted operation in Lyari to flush out the criminals.
He also warned opposition party leader Nawaz Sharif against including Uzair Baloch the leader of the Aman committee in the PML N party.
"He is a criminal and action will be taken against him. There will be no talks with criminals and terrorists," Malik said.
Uzair Baloch who was a close associate of former home minister, Zulfiqar Mirza who had resigned last year due to differences with the government