All those being held have been involved in discussions about the church's planned annual conference.
Fiji's military government has already banned the meeting once, accusing the church of being too political and setting conditions for future talks.
The Methodist Church is the largest in Fiji and hopes to hold its annual meeting next month regardless.
The church had hoped its leaders would have been released after a few hours, Radio New Zealand reported.
Instead, police, many of whom are themselves Methodists, were treating the churchmen well in detention, Radio Australia reported, with afternoon tea and a prayer.
But the interim military-led regime has banned the gathering unless the church hierarchy agrees to exclude two former presidents and remove any political discussion from the agenda.
Among those arrested was former president of the Fiji Methodist Church, Reverend Manasa Lasaro; General Secretary, Reverend Tuikilakila Waqairatu, the Secretary for Pastoral Ministry, Tomasi Kanailagi and the Church's Finance Secretary Viliame Gonelevu. The general secretary was taken in on Tuesday night and others were detained the next morning.
The Chief of Rewa, Rotemumu Kepa, who was to host the conference, has also been arrested and detained.
The interim government authorities have not explained the detentions, but Reverend Waqairatu had earlier said that it was in relation to conference.
The church said it was planning to go ahead with the conference regardless of the interim government's stand.
Separately, Fijian police are reported to be holding on to the wands, compasses and a skull confiscated from a Freemasons' meeting in Denarau last week.
The police said all the 14 masons detained had been released but that investigations into their activities were continuing.
Fiji is currently ruled by Commodore Frank Bainimarama who took power in a coup in 2006.
Since then Fiji has suspended the constitution, detained opponents and suppressed freedom of speech.