European countries all seem to have some type of "ministry of culture" that tends to hold sway over some of the more historic examples. My understanding is that the rather famous organ at St. Bavo's in Haarlem, Holland is owned by the CITY, which strikes me as a somewhat odd arrangement. Once they become the European equivalent of 'historic monuments' the bureaucracy has as much to say about them as anyone else. Or at least so I understand.
This is (partly) correct.
'My' organ (or at least the one I'm in charge of), is such a case. It is owned by the State, like many historical organs in several European countries. This has happened because of ancient (often Napoleontic) law, valid not only for several organs, but also other church property of all kinds.
As a consequence, the organ in this case is owned by the State and 'in the care of church x or y'. So finally the church has to come up with the money for usual maintenance. It happens that the city contributes to it, somehow.
The real nastiness starts when overhaul or restoration is in order. On this organ here, the State would contribute 90% of the hefty cost if everything is approved. However, the State then controls everything. We (organist, consultant, council) barely have any say in the matter. The real killer is that the cheapest subscribing organ builder gets to do the work. In the case of a valuable historic instrument, this is mostly a disaster waiting to happen. Firms really capable of restoring / overhauling that kind of organ know what price to ask for their expertise. Never a rock-bottom price. So, in this system you never get quality.
As a consequence, the in fact necessary restoration of the organ has been postponed indefinitely, as it may turn into ruins what still stands today - my ultimate nightmare. There are numerous examples of horrible restorations all over the country. Unfortunately, some day it'll be a non-choice ...