In 1996, Qureshi retired from PAEC as Chief Scientific Officer and was made scientist emeritus, which allowed him to continue research at PINSTECH before moving to Karachi. He took up the professorship of chemistry at the Karachi University and headed the nuclear chemistry section at the H.E.J. Research Institute of Chemistry. During this time, he authored several articles and published books on nuclear chemistry. He retained his position till 2001 when he joined the Pakistan Nuclear Regulatory Authority (PNRA).
At PNRA, Qureshi served as the chief scientific officer and adviser to the government on nuclear policy issues. His contribution and policy efforts led to the physical security of the commercial nuclear power infrastructure in the country and helped launched the nuclear awareness campaign following the Fukushima nuclear disaster in 2011. He served until 2009 when he decided to accept the professorship of chemistry at the Institute of Engineering and Applied Sciences. In December 2012 Qureshi had a sudden breathing problem and died. He is buried in Karachi, Sindh.