The Methodist Church says it was told the organ had to be removed from a church in which three workers died during the February earthquake, in order to strengthen the building.
The Durham Street church was red stickered following the first quake on 4 September 2010 and the three men were trying to dismantle its organ when the 22 February quake occurred.
Methodist Church representative Gregory Wright told the Canterbury Earthquakes Royal Commission on Tuesday that engineers said there was some risk involved in removing the organ.
But Mr Wright said he was told the risk was not enough to stop the work being done.
He said he was advised the organ had to be taken out so that internal temporary propping could be put in place to strengthen the building.
Six men were in the unreinforced masonry building dismantling a pipe organ when the quake struck, but only three made it out alive.
Laura Nicol, the sister-in-law of one of those killed, told the Commission she believed there had been a breakdown in safety processes and that the safety aspect had been underrated as a whole.
"In hindsight we can all say, should anyone have been in that building, and that's the big question."
But the site's project manager says he was comfortable with the safety of the building and the engineers followed the correct processes.