His family decided to cremate Richard Frye's body on June 8 after Iran failed to comply with his request, the Tehran Times daily reported, citing the academics Iranian colleague Turaj Daryaie.
Frye, a Harvard University professor who dedicated his life to studying Iran, said in his will that he wanted to be buried on the banks of the Zayandeh Rood river in the central city.
He died aged 94 in Boston in March.
A group of people in the city also protested outside a site gifted to Frye by former president Mahmoud Ahmadinejad in 2010, which would have been his burial place.
Ahmadinejad gave official approval to Frye's wish to be buried in the country.