The moderate Rouhani, who is expected to stand for a second four-year term in the May vote, has targeted the judiciary in a series of public statements over the case of a billionaire businessman on death row for corruption.
Judiciary chief Ayatollah Sadegh Larijani has hit back with accusations of his own, and today supreme leader Ayatollah Ali Khamenei made reference to the dispute.
In a speech to thousands of people in the religious city of Qom, Khamenei alluded to "recent arguments" among powerful figures, adding: "This will be resolved with the help of God."
Zanjani was arrested in 2013, three months after Rouhani took office pledging a crackdown on corruption.
He rose to prominence after sanctions were imposed on Iran over its nuclear programme, boasting in media interviews of finding ways around banking restrictions to ensure Tehran continued to receive money for international oil sales.
In his speech, Rouhani appeared to suggest that the judiciary had not done enough against others potentially involved in the case or to recover funds embezzled by Zanjani.
The death sentence against Zanjani was "very well", Rouhani said, "but what becomes of the money?"
Last week Larijani hit back, defending the judiciary's handling of the case and criticising the government for not doing enough to help track down missing funds.
"It should not be implied that the judiciary has done little on this case," Larijani said, insisting it was working "to recover the misappropriated money".
"The case remains open... We have summoned former ministers and the former director of the central bank," he said.
Iranian authorities have so far only been able to recover about USD 600 million of the embezzled money from the seizure of Zanjani's assets in Iran.
Larijani called on the foreign ministry to demand information on the funds from the governments of Malaysia, Turkey, Tajikistan and China. The ministry replied that it had given its "full cooperation" to the judiciary.
Larijani also revealed claims made by Zanjani during his questioning that he had paid hundreds of thousands of dollars to presidential candidates in 2013.
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