Pastor Matthias Haghnejad, pastor Behnam Irani and deacon Silas Rabbani from the Church of Iran have been held separately at Ghezal Hesar Prison after being accused of 'Mofsed-e-filarz', or 'spreading corruption on earth'.
Despite the charges being dropped, all three men have been tried for "action against national security" and "creating a network to overthrow the system".
The men now await a verdict from Judge Asel Al-Hosseyn, who tried their cases.
CSW chief executive Mervyn Thomas said: "While we applaud the dropping of the capital charges levelled against pastors Haghnejad and Irani, and deacon Rabbani, it is completely unacceptable that they have faced trial once again on unwarranted charges and that their unjust prison terms may be extended even further.
"Moreover it is difficult to conceive of how imprisoned men from a severely repressed community could pose a danger to such a powerful system."
Elsewhere, three of six Christians arrested in Isfahan in early September have been released.
Moluk Ruhani, Zainab Akbari and Hamidreza Borhani were released in late September, while Mohammed Taslimi and Parsa Dadkhah remain incarcerated.
The whereabouts of Moluk Ruhani's sister, Sepideh Morshedi, are unknown.