Persepolis has recently parted ways with Juan Carlos Garrido and is looking for a replacement for the Spaniard until the end of the season.
Kovac, 53, would rather take up a position at one of Europe's leading clubs, media reported.
Karim Bagheri has been appointed as interim coach at Persepolis.
The defending champion sits fourth in the Iran league, five points behind leader Tractor.