The action was prompted by the preliminary report on the crash of the PIA aircraft in Karachi last month, which found that pilots failed to follow standard procedures.
Global safety and transport bodies expressed concern over the alleged dubious licences and said they were looking into the matter.
Malik had also informed the aviation ministry about the flight safety measures. The 262 pilots 109 commercial and 153 airline transport pilots were grounded on Friday, pending conclusion of inquiries against them. They included 141 from PIA, nine from Air Blue, 10 from Serene Airline, and 17 from Shaheen Airlines, which has closed down, the report said.