Grand Ayatollah Nasser Makarem Shirazi questioned the competence of Esfandiar Rahim Mashaie to hold office over his comments, which sparked fury among conservative MPs, Islamist student groups and some clerics.
"There is no doubt that the Israeli regime and people are both against Islam and Muslims, occupying their lands… so how could we speak of friendship with them?" Marakem Shirazi was quoted as saying by the conservative Jomhuri Eslami newspaper.
"Why should people who think like that be one of the president's colleagues?" he added.
Rahim Mashaie, vice president in charge of tourism, is one of Ahmadinejad's closest allies and earlier this year his daughter married the president's son.
"I have said before that we do not have any hostility against the Israeli people and I still say the same thing proudly," he said in remarks published in several local newspapers last week, echoing statements he also made in July.
