MacMillan, who was commissioned to compose much of the music for the visit of Pope Benedict XVI to the UK in September 2010, has established a new body, Musica Sacra Scotland, which held its first conference in Glasgow last year.
He said critics of the body had accused him of wanting to take music in the Mass "back to the Middle Ages".
The composer would like the new organisation, formed with the violinist Paul Livingston, to encourage church-goers, priests and parishes to use chant-based sacred music, both ancient and newly composed.
He said that, despite internal critics, it is "nothing to do with politics". MacMillan said the drive to revive "very simple" chant-based music in church has proven controversial, with some seeing it as a critique of the popular-music influenced music used in services since the reforming Second Vatican Council of the mid-1960s.
Since 2005, MacMillan has been associated with the parish of St Columba's in Maryhill, Glasgow, and has formed a small choir which helps lead worship at Mass there on Sundays.
But the composer, who recently toured India with the BBC Scottish Symphony Orchestra, said the bid to promote chant-based music in worship is not about church politics.
He said: "This is very simple music we are talking about, simple chant in English, and I think there is an aesthetic need for a simple beauty in the Mass.
"There is a lot of music in the last 40 years which has borrowed very much from certain types of popular music, that when it is translated into the church sounds banal and embarrassing, and we are not in the business of trying to throw that all out, but we are wanting to posit something different, just in case people forget about what the roots are."
The composer said the idea of returning to chant-based music is not restricted to those concerned with music in the Catholic church.
"There are similar arguments in other churches, but there is not the same kind of strange spectral politics at the back of it, which there shouldn't be with us and isn't actually," he said. "Anglicans wanting good music and liturgy can be liberals or conservatives.
"But with our argument it is seen as conservative, which it is not necessarily: I am just a normal Catholic. But there is a certain group, who are set in their ways, who are in a certain age group. They were young in the 1960s.
"Vatican Two was a great thing, but it was promoted by those who were most enthused at the time, and they have become entrenched and they see dangers when there are none there."
MacMillan added: "It is just a case of trying to ameliorate that and trying to convince them that it is nothing to do with politics or 'trying to take us back to the Middle Ages'. I think there are parallels in all the denominations actually … you are painted as a killjoy, but the young people don't want all that [newer music]. They find it embarrassing."
The composer and conductor declined to comment in detail on the coming independence referendum, saying: "It's not my topic. I watch it with interest, but I have no inclination to get involved."