Akram's comments follow a warning issued to Akhtar by the Pakistan Cricket Board (PCB) on Saturday telling him to improve his conduct while playing for the national team.
"The medical inquiry was a big mishap. We should have avoided it. (It was carried out) Simply because India was a better team and they beat Pakistan," said Akram on Sunday.
Doubts had been raised over an injury Akhtar claimed during the decisive third and final Test against India in Rawalpindi after he hurt his wrist and back in a fall on his follow through on the second day.
The 28-year-old Akhtar did not take the field on the third day, but his coming out to bat seemingly unaffected on the fourth day raised suspicions over the extent of his injury.
He and three other Pakistani players appeared before a four-member medical commission formed by PCB to assess a spate of injuries to Pakistani players during the third Test which Pakistan lost by an innings and along with it the series 2-1.
Akram, a veteran of 104 Tests and 352 One-dayers for Pakistan, said: "I think the captain, coach and the manager should handle a player and it should not happen like this. How can you assess an injury after two weeks.
"Nobody knows where the medical commission's report is and what the aim of the inquiry was."
Akhtar who left for England on Sunday to play for Durham County said, "I will have a rest and scans on my injuries before I regain full fitness to play for Durham. No player can imagine faking an injury and I always take pride in playing for Pakistan."
Akhtar made his Test debut under Wasim Akram against the West Indies in 1997-98.