IHF says in a statement the charges brought against Habibullo Nasrulloev are "politically motivated."
Tajik prosecutors say the former minister, who fled Tajikistan in 1997, was involved in an armed plot to overthrow President Imomali Rakhmonov's government.
They also say Nasrulloev is wanted for murder and participation in gangs.
On August 21, the Moscow City Court vetoed a Russian prosecutor-general's extradition petition.
IHF is urging the Russian authorities to ensure Nasrulloev's prompt release and provide him with the necessary protection to avoid any acts of reprisal against him.
Nasrulloev's Russian lawyer, Anna Staviskaya, has said her client will appeal to the European Court of Human Rights over his "illegal detention."
Under Russian laws no one can be held in custody without trial more than 18 months.
Nasrulloev was arrested in Moscow in August 2003 under a Tajik arrest warrant.
He did not appear before a court until 2006.