She said Khamanei's remarks were "clear interference in the internal affairs of the Palestinian people, continuing efforts on the part of the Iranians to undermine the Palestinian Authority."
Earlier Wednesday, Khamenei said in an address to open a two-day global summit Tehran organised in aid of Gaza and the Palestinians that "the only way to save Palestine is resistance.
"Support and help to Palestinians is a mandatory duty of all Muslims. I now tell all Muslim brothers and sisters to join forces and break the immunity of the Zionist criminals."
But Khamenei's call was bluntly dismissed by president Mahmud Abbas after he met Clinton, who before arriving in Europe had taken part in her first visit to the Middle East since taking office.
"We are sending a message to the Iranians and others — stop interfering in our affairs," Abbas said. "They are interfering only to deepen the rift between Palestinians."
Clinton applauded the response from Abbas.
"President Abbas responded appropriately to what were comments made at the highest level of the Iranian government today," she said. "I think he spoke forcefully on behalf of his people and the Palestinian government."
