Bishop Christopher Budd is fully behind the £1 million refurbishment plans, which include ripping out the cathedral's oak pews, only installed during the last 12 years.
But the plans were attacked last week at a meeting of 130 parishioners, one of whom described the mood of the meeting as "passionate some elderly people were in tears".
A member of the parish council said: "They intend to replace the pews, which were paid for by public subscription, with chairs which face each other, rather than the sanctuary."
The proposals also include moving the lectern from the sanctuary to the other end of the cathedral and replacing the existing baptismal font with one for full immersion.
One parishioner said "we feel we are being led by the nose by other faiths".
Out of the 12 members of the parish council. there were 10 no votes and two abstentions. One council member said: "What the parish council and the parishioners want is the same thing a new committee for re-ordering the cathedral that includes more members of the laity."
Feelings in the congregation are running high over the estimated million cost of the refurbishment, which will include new accomodation for the bishop and the building of a new parish centre.
"We are in a deprived inner-city area and this seems blatant and extravagant change, simply for the sake of it," said one parishioner.
Plymouth cathedral was devastated during the last war and few old buildings remain. Many members of the congregation feel that plans to modernise the Victorian cathedral are, as one man said, "tantamount to vandalism".
Bishop Budd was um:vailable for comment, but Fr Robert Plant, a member of the archdiocesan committee which proposed the re-ordering, stressed that "there are no final plans". He declined to comment further.