Pastor Matthias Haghnejad and two members of the congregation were detained early on Saturday morning by Iranian security authorities.
It's not yet clear where they are being held and it's thought several bibles, religious leaflets and a computer were also taken by officers.
The pastor has been targeted in the past - he's been jailed on three other occasions.
Christian Solidarity Worldwide Chief Executive Mervyn Thomas said, "CSW is deeply concerned at the news of arrests of Pastor Matthias Haghnejad, Mohammad Roghangir and Suroush Saraie, and the fact that their current whereabouts remain unknown.
"These men have been targeted by the Iranian authorities in the past, and despite the political charges being levied against them, they were clearly arrested on account of their faith.
"We urge the Government of Iran to halt its harassment and imprisonment of religious minorities and to uphold freedom of religion or belief, as outlined in covenants to which Iran is party.
"In addition, the international community must hold Iran to account for the well-being of prisoners of conscience, and particularly that of Mr Soltani, who was convicted on charges an independent court would have rejected, The Iranian government must ensure as a matter of urgency that Mr. Soltani receives the medical attention recommended by the physicians that examined him."