Khamenei is accusing the West, specifically the United States, of stirring up trouble by trying to create a division between the regime and the populace.
The BBC said the number of student protesters increased after U.S. satellite television broadcasts urged people to gather at Tehran University.
But during an address to a crowd of several thousand in the town of Varamin in southern Iran, the BBC said the ayatollah warned America was trying to turn disgruntled people into mercenaries to cause trouble.
He appealed for calm but also said if necessary he would call on his supporters to deal with the troublemakers. He added: "Leaders do not have the right to have any pity whatsoever for the mercenaries of the enemy."