Iran's conservative-controlled parliament had earlier in August blocked a proposal, put forward by the government, to give a legal definition of political crimes.
Ayatollah Mahmoud Hashemi Shahrudi was quoted as saying it was now up to his powerful institution to step in, given the issue was a "judicial matter".
"Unfortunately, political crime, which is a legal issue, is taken as a political one," he said.
Human rights activists say a legal definition of political crimes is required so that those who are convicted because of their political beliefs are not punished under common law.
The crime of undermining state security is frequently used to imprison those opposed to the Iranian regime.
Iranian courts, considered a bastion of conservatism in the Islamic Republic, deny that political prisoners exist in Iran as political crimes are not defined.