However, the man who made the one submission received against the registration warns the news could mean the parish council will "not be able to do a jolly thing" with the crumbling church, which is more than 100 years old.
"It's very restricting," church finance and works committee chairman Graeme Flett said.
At a recent Wellington meeting, the trust board also approved category 2 status for South Dunedin's former King Edward Picture Theatre, now known as the Mayfair Theatre.
Trust Otago/Southland area manager Owen Graham said both landmarks had considerable heritage value and their registration underlined how important they were to the Otago region.
The response from the Milton community in wanting to formally recognise Tokomairiro Church was phenomenal, he said.
"In cricketing terms, 504-1 is a pretty convincing total. And it's the same in heritage terms."
The church, built in 1889, was designed by architect Robert Arthur Lawson, whose work included Dunedin's Municipal Chambers and First Presbyterian Church.
Parish Council treasurer Marion McGuigan said she was pleased but there was a lot of work ahead.
The parish would this week discuss forming an action group to seek funding for church restoration.
The King Edward Picture Theatre was opened in 1914 and was the oldest surviving purpose-built theatre in Dunedin.
It is now used as a live theatre venue.
Mr Graham said the theatre was one of the oldest surviving examples of a large suburban theatre.
"Given the history and prominence of this South Dunedin landmark, it is appropriate its heritage value has been recognised."
Mayfair Theatre Trust chairman Les Cleveland said the registration would safeguard the history and style of the building for the future.
Registration is designed to assist protection of historic places under the Resource Management Act 1991.
