A spokesman from Pakistan's Foreign Office, Abdul Basit, told the BBC that Shahram Amiri was seeking immediate repatriation to Iran.
In June videos purportedly of Mr Amiri but containing contradictory information on his whereabouts emerged.
The US rejected Tehran's claims that it was behind Mr Amiri's disappearance.
With his third stage win this year the French three-time winner of the race holds a two minute and 28 second advantage on his main rival Marc Coma.
Spain’s Coma, who took the lead on Monday, was second on the day three minutes and 54 seconds back but he remains well in contention to defend his title.
But earlier this month, Tehran said it had proof he was being held in the US.
The allegation came after three videos purportedly of Mr Amiri emerged - the first said he had been kidnapped, the second that he was living freely in Arizona, and the third that he had escaped from his captors. u • • • ferreira A missing Iranian nuclear scientist, who Tehran says was kidnapped a year ago by the CIA, has taken refuge in the Iran section of Pakistan's US embassy.
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