Does your church as an organ but your pastor or priest is against using it in the liturgy? Does he prefer guitars, piano and synthesizers?
This is not uncommon these days.
If your church has an organ and if you truly love your instrument, you have to find a way use it. Maybe not for liturgy at first because your pastor doesn't like it right now. You'll have to work towards changing his feelings which is a difficult task.
First, you have to earn his trust which can be don over time by helping him in some way.
Perhaps he might reconsider when he sees that people like it and demand it.
So you might want to prepare and play a short concert or organ demonstration.
Think of why he doesn't like the sound of the organ - mixtures, too loud, to screaming sound, too powerful reeds? Maybe it reminds him of funerals. I don't know. Maybe start gentle and soft.
Usually when they say they don't like the sound of the organ, they probably mean something different. You'll have to find out what that is. I think it might be the quality of the music he was accustomed to hearing in church was rather low than the sound itself didn't work for him.
Use flutes and strings for now.
Let him often find you "accidentally" practicing some very sweet and gentle music which only very spiritually stubborn people can resist. I think he can do better than that.
[Thanks to Isabel]