"Someone made a statement about people who live in Israel. It was an inaccurate statement," Khamenei said in his sermon on Friday at the main weekly Muslim prayers in Tehran.
"To say that we are friends of the Israeli people like all the other people of the world is not fair comment, it is an illogical comment," he said in the sermon broadcast live on state television.
"Someone said something false and there were reactions. These should end," the leader said, calling on opponents of the government to end debate "on this minor question."
Khamenei said Israelis have "usurped the houses, land, fields and businesses" of Palestinians.
"It is Israeli people who inhabit the settlements… and which the puppet Zionist government arms against the Palestinians," he said.
"The Islamic republic's position is very clear… We have no problem with Jews, Christians or the faithful of other religions, but we have a problem with the usurpers of the land of Palestine," he said.
A few hours later Mashaie, a vice president in charge of the tourist board, issued a statement saying he fully respected the Khamenei's policies.
"I act within the framework of the policies defined by the supreme leader," said his statement as carried by the official IRNA news agency.
Later lawmaker Ali Motahari also announced that he was dropping plans to petition Ahmadinejad to address parliament on the issue.
Mashaie said in mid-July that Iran is a "friend of the Israeli people." He returned to the theme in August, saying he had "no hostility against the Israeli people."
His remarks prompted fierce criticism from leading religious and political leaders, notably in his own conservative faction, which called for his dismissal.
On Thursday, Ahmadinejad, whose son is married to Mashaie's daughter, defended his associate by insisting that he had been misquoted by the media and never made the offending comments.
Ahmadinejad also rejected the views of religious leaders on the topic.
