"Your actions and words show you don't want us to have the Arak heavy water reactor which means you want to deprive us of our rights," Salehi was quoted as saying by the website of state broadcaster IRIB.
"But you should know that it is a red line which we will never cross, likewise enrichment" of uranium.
Arak is of concern because, in theory, it could provide the Islamic republic with plutonium -- an alternative to highly enriched uranium used for a nuclear bomb.
Iran also committed for six months "not to make further advances" at its Fordo and Natanz uranium enrichment sites and at Arak.
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Abbas Araqchi, a deputy foreign minister and member of the nuclear negotiating team, insisted Arak "should remain as a heavy water power plant", the official IRNA news agency reported.
Tehran has invited the UN atomic watchdog to visit the Arak site on December 8, for the first time since August 2011.
Salehi also rejected the charge, saying "Arak's reactor does not produce the type of plutonium suitable for a bomb".
"We want to have more heavy water reactors in future," he added.
In the Geneva agreement, Tehran reaffirms "that under no circumstances Iran will acquire or develop nuclear weapons" and build no "reprocessing factory" essential to purify plutonium so it can be used to make nuclear weapons.
The United States said one of the key points of the Geneva agreement is that Iran commits not to build a facility capable of reprocessing.