I recently spent two weeks in Istanbul and encountered very little evidence of pipe organs. Instrumental and congregational music are not part of Islamic prayer, so the lack of organs was not surprising. The two Roman Catholic Churches in the Galata district house functional pipe organs which I saw but did not hear (see photos). The Christian Orthodox churches do not have organs.
One of the universities contains a concert hall with a 6000-pipe organ, but I did not see this one. I do not believe the modern civic concert hall houses an organ. Turkey does not have, obviously, much of an organ culture.
We do know of a 16th century instrument built and installed by English organ builder Thomas Dallam for the Ottoman Sultan Mehmed III at the behest of Queen Elizabeth. I had read that this was no longer in existence, but while touring the mid-19th century Dolmabahçe Palace I noticed remnants of pipes and organ mechanisms in a large, glass fronted cabinet. Unfortunately, no photography is allowed in the palace. Read more about The Sultan’s pipe organ.
I was in a clock museum and saw a musical clock (such as Haydn and Mozart knew). Most of the internal pipes, however, were crushed.