The three-member bench of the Supreme Court of Pakistan told Brig Faheem to carry on his investigation of Ali Musa Gilani and co-defendant Khushnood Lashari, Pakistan's Geo News reported Tuesday.
The two are accused in the illegal sale of $77 million worth of the controlled substance ephedrine.
Brig Faheem told the court both defendants managed to flee the country because their names were not included on an exit control list in a timely fashion.
The request to replace the investigating officer was filed by Gilani's lawyer.
Musa Gilani Monday gave contradictory statements to the Supreme Court and the anti-Narcotics Force about Brig Faheem, court observers said.
He told narcotics investigators he had no problems with Brig Faheem, which contradicted other testimony.