Benham Irani is was first arrested in 2006 and sentenced in 2011 for actions against the state.
Christian Solidarity Worldwide says he's being held in solitary confinement and is facing 18 new charges, including "Mofsed-e-filarz", translated as "spreading corruption on Earth" which carries a sentence of death.
In June, Pastor Irani was removed from prison and temporarily held in solitary confinement where he was interrogated on five occasions for four hours each time.
CSW claims he was warned that if he did not obey he would receive a further sentence and remain in prison for a longer time.
The charity thinks the fresh charges are part of a crackdown on religious and ethnic minorities in Iran.
CSW's Chief Executive Mervyn Thomas said: "We are deeply concerned by the new charges against Pastor Irani, especially the charge of spreading corruption on Earth, which bears unsettling similarities to the one faced by Pastor Matthias.
"Such charges are tantamount to an indictment of Christianity itself and mark a renewed escalation in Iran's campaign against Persian Christians under the Rouhani presidency.
"It is also deplorable that a prisoner of conscience like Farshid Fathi is currently held with hardened criminals.
"We urge the Iranian government to transfer him to an appropriate ward as a matter of urgency and put it on notice that it will be held accountable for his safety.
"We also call on the government to drop the unwarranted charges against Pastors Irani and Haghnejad, and to release them, along with the five Christians arrested this week and others who have been unjustly detained on account of their faith and in contravention of international covenants to which Iran is party, that guarantee freedom of religion or belief."