Younis was asked by the Pakistan Cricket Board (PCB) to take over the job after Inzamam-ul-Haq stepped down and retired from one-day internationals last month.
But Younis felt the job was too stressful, especially in the wake of the hostile reception given to the players after the Caribbean debacle.
"I don't understand it. If he didn't want to be captain he should not accepted the vice-captaincy for the last two years," Imran told Reuters on Tuesday.
"His refusal has led to a crisis."
PCB sources told Reuters all-rounder Shoaib Malik would become the next captain following Younis's decision.
"It is useless trying to convince Younis to lead the team if he does not want to do it. But what he did was wrong," said Imran.
The cricketer turned politician, who led Pakistan to their only World Cup triumph in 1992, said he wished Malik the best.
"He appears to have a good cricket brain and could turn out to be a very good choice for Pakistan cricket.
"I hope he has the ability to accept the challenge. It could make him into a better player and bring out the best in him."
Another former captain, Javed Miandad, also criticised Younis.
"This episode is a reflection on the sort of discipline prevailing in our cricket set-up," he said.
"It is disappointing for me that someone should turn down the honour of being asked to captain his country. It is not a good sign for Pakistan cricket."
