"The country is run on ad hoc basis and so is cricket, and I think ad hocism has to finish," Khan told AFP on Sunday.
Pakistan cricket, run by ad hoc bodies since 1999, has been in the spotlight since August's Oval Test against England when captain Inzamam-ul Haq refused to take his team back on the field after it was accused of ball-tampering.
Inzamam was acquitted of tampering but was handed a four-match ban for brining the game into disrepute. His replacement Younis Khan last week refused to lead the side, saying he did not want to be a "dummy" captain.
The refusal prompted Pakistan Cricket Board (PCB) chairman Shaharyar Khan to resign. His successor Nasim Ashraf reinstated Younis on Saturday, hours before the team's departure for India and the Champions Trophy.
Khan said recent events showed that Pakistan had to change the way cricket is run in the country, in particular its policy of allowing the president to pick who will lead the Board.
"It's a tried and failed system because the cricket chief is not accountable to anyone no matter how many blunders he makes," he said.
The 53-year-old Khan, who is now a member of national parliament after switching from cricket to politics in 1995, is a vociferous critic of the military-led government.
"Elected associations should elect the chief which happens everywhere in the world."
Khan's former teammate and legendary batsman Miandad said recent incidents showed the relationship between the Board and the players was breaking down.
"I can't understand what has been happening. It's the lack of fear of the Board and selectors. Board had encouraged indiscipline and players have little respects for their superiors," said 49-year-old Miandad.
Miandad urged the new cricket chief to take drastic action to repair the situation.
"For posterity we will have to purge the dirt and make the base and the Board strong.
"Why did the Board tolerate indiscipline. Australians did not tolerate Shane Warne's indiscipline even though he is so important to them," said Miandad, also a former coach.
He also questioned the reaction of Bob Woolmer, Pakistan's English coach, to the highly charged atmosphere at the time of the Oval standoff.
"Woolmer's character was questionable in the Oval fiasco. Team was under pressure because of the events and he talked about resigning," said Miandad.