The appointment by Ahmadinejad last week of Esfandiar Rahim Mashaie as his first deputy has sparked a chorus of opposition from conservatives in Iran, who were outraged when he made pro-Israel comments last year.
"We support the president… but we never said that he has no flaws," Ahmad Khatami told worshippers in his Friday prayer sermon which was broadcast live on state radio.
"We wish it had never gone this far so that the leader (Khamenei) comments on it. We conscientiously told you (before) to revise the appointment of first vice president," he added.
"Now that the leader has expressed his opinion, there is no room to hesitate," Khatami said, indicating that the supreme leader wants Rahim Mashaie to be dismissed.
Khatami urged Ahmadinejad to "obey (the leader) in the quickest time."
Several Iranian officials have in recent days said that Khamenei has expressed his opposition to the appointment of Rahim Mashaie, but this has not been officially confirmed.
Attempts by AFP to obtain clarification from the supreme leader's office and from Ahmadinejad's aides have proved fruitless.
Additionally, Iranian state media, including the official IRNA news agency, has not reported Khamenei's opposition to Rahim Mashaie's appointment.
Rahim Mashaie, whose daughter is married to Ahmadinejad's son, is an outspoken figure who last year earned the wrath of many, including Khamenei, for saying Iran was a "friend of the Israeli people."
A defiant Ahmadinejad has so far shown no sign of reversing his decision, despite a growing call to do so from hardline clerics, politicians, Islamist students and MPs, among them even his own supporters.
"I like Rahim Mashaie for 1,000 reasons. One of the biggest honours of my life and one of the biggest favours from God to me is knowing Rahim Mashaie," the president said on Wednesday.
"He is like a pure source of water," Ahmadinejad added. "He is like a transparent mirror. Unfortunately not many people know him."
