Archbishop of Cardiff Peter Smith says the plans could deprive Catholic parents in Merthyr and beyond of a suitable school for their children.
Students at Bishop Hedley Catholic High in Merthyr have staged a silent protest at the council's proposals.
But Merthyr council says the status quo is "not an option."
The council wants to replace the sixth forms with an expanded tertiary college at a "Merthyr Learning Quarter" on the site of the present Merthyr Tydfil College.
Four sixth forms would close at Cyfartha, Afon Taf, Pen y Dre and Bishop Hedley schools.
Staff and students at Bishop Hedley say the plans will mean an end to post-16 Catholic education in their Catholic deanery area, which takes in parts of Blaenau Gwent, Caerphilly and Rhondda Cynon Taf as well as Merthyr Tydfil county borough.
Year 12 student Bethan Morris, 17, said: "We feel as a school that that is particularly unfair. It's just going to be lost with the tertiary college."
Students at Bishop Hedley staged a silent protest as education officials arrived at their school for a consultation meeting on the plans.
Similar protests have been held at Afon Taf and Cyfarthfa schools.
Bishop Hedley's head of community focus education Bill Mulry called it a "very dignified but a very peaceful protest", which he said had been organised by students with the permission of the head teacher, Maureen Harris.
In silence, students formed two lines opposite each other for a length of around 200m from the gates of the school, down a corridor, to the room in which the meeting was to be held.
Parents' rights
Archbishop Smith said even if the redevelopment of tertiary education in the borough goes ahead, Bishop Hedley should still be allowed to retain its sixth form.
He said: "It needs to be recognised that Catholic parents have a right to have their children educated in accordance with the teaching of the Catholic Church."
"That would be a huge loss to the quality and diversity of education in the area and deprive Catholic parents of a suitable school to educate their children according to their wishes.
"Since the 1944 Education Act the Catholic Church has worked very successfully in partnership with national and local government.
"It would be a great pity if that partnership were to be seriously damaged by any refusal to recognise the legitimate needs of Catholic parents."
The Welsh Assembly Government declined to respond to the archbishop's comments.
'Cannot be complacent'
A spokesperson for Merthyr council said: "It is clear from performance in Merthyr Tydfil that we cannot be complacent about the need for improvement. In short, maintaining the status quo is not an option.
"The proposals for removing sixth forms in Merthyr Tydfil and establishing a tertiary college are in response to the Welsh Assembly Government's policy for transforming learning and training in Wales.
"They are aimed at lifting the standards achieved by the full cross-section of young people aged 16 to 19 as well as at benefiting performance for all pupils aged 11 to 16."
The spokesperson added that the proposals are being tested for appropriateness through the consultation meetings.
She said a report would be prepared summarising the outcomes of the consultation and highlighting any viable alternatives.
+++++++++++++++++++++++++++++++++++++++++++++
Disclaimer
No responsibility or liability shall attach itself to us or to the blogspot ‘Clerical Whispers’ for any or all of the articles placed here.
The placing of an article hereupon does not necessarily imply that we agree or accept the contents of the article as being necessarily factual in theology, dogma or otherwise.
SIC: BBC