According to Christian Solidarity Worldwide (CSW), police smashed the front door of the pastor's home on Sunday, punched him and his teenage son Daniel and used electric batons on them.
Pastor Nadarkhani was then reportedly taken to Evin prison.
The incident happened as the pastor was on bail awaiting a summons to prison following the failure in May of an appeal against his conviction.
Fellow Church of Iran members Mohammadreza Omidi, Yasser Mossayebzadeh and Saheb Fadaie were also involved and charged with "acting against national security" by "promoting Zionist Christianity".
The four men had been given ten year sentences but Pastor Nadarkhani and Mr Omidi got an additional two years each, to be served in remote and inhospitable locations in the south of the country.
They were all arrested in May 2016 during a series of raids by security agents on Christian homes.
They were found guilty in July 2017 by a judge who, according to CSW, is accused of "overseeing miscarriages of justice" and is subject to financial sanctions in the United Kingdom.
Their appeal hearing in December 2017 took place before Judge Hassan Babaee and Judge Ahmad Zargar, both of whom are alleged to have played prominent roles in the crackdown on freedom of expression in Iran.
CSW's Chief Operating Officer Scott Bower said: "The national security charges levelled against these men were spurious, and their sentences are excessive, amounting to a criminalisation of Christian practice.
"We are calling for the unconditional release of Pastor Nadarkhani and for his sentence and those of Mr Omidi, Mr Mossayebzadeh and Mr Fadaie to be quashed."
Lawyers representing the four Christian men were notified by text message of the failure of the appeal by the Iranian authorities in Rasht on 2 May 2018.
Bower added: "The international community must press the Government of Iran to uphold its constitutional obligations towards its Christian community and to respect the right of its citizens to the full enjoyment of freedom of religion or belief, as outlined in the International Covenant on Civil and Political Rights, to which it is signatory."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.
