Yousef Nadarkhani's wife Tina Pasandide Nadarkhani, and fellow church member Yasser Mosayebzadeh, have also been held.
Pastor Nadarkhani was initially arrested and charged with apostasy in 2009, after going to his children's school to call the Muslim monopoly on Iranian education unconstitutional.
He was sentenced to death in 2010, a decision that was upheld by the Supreme Court in 2011.
The pastor repeatedly refused to renounce his faith during court hearings, in order to avoid the death penalty, and was released in September 2012, after his acquittal on apostasy charges.
He was, however, convicted of charges of evangelising Muslims, for which he received a three-year sentence.
Pastor Nadarkhani has previously been re-arrested since his release from prison in September 2012.
On Christmas Day 2012 he was re-arrested to serve the remainder of a three-year sentence and was released once again the next month.
Christian Solidarity Worldwide's Chief Executive Mervyn Thomas said: "We are deeply concerned by these developments and await further clarification regarding the reasons for these arrests.
"Unfortunately, it is not uncommon for Christians who have been arrested on account of their religious beliefs to be released and re-arrested time and again.
"We once again call on Iran to fully respect its constitutional and international human rights obligations by ensuring that justice and equality before the law are guaranteed to all citizens, regardless of their religion or belief."