Organ expert Martin Kares, who serves on the board of the German Association of Organ Experts, said churches had been slow to sound out the problem, which he estimates affects about five percent of organs in the country.
"The problem has been known about for the last 15 years," he said. Kares blamed the mould on poor ventilation, saying that with fewer caretakers, the routine of airing out church rooms had changed.
The local church in the northern city of Gardelegen is just one of many in Germany with a mouldy organ. Organ-builder Jörg Dutschke has been working to rid the instrument of the fungal growths, which he refers to as "haemorrhoids".
Dutschke has to wear a surgical mask to protect him against the mould. To fix the instrument, he has to take it apart, clean it and treat it with fungicide - a massive undertaking, since the organ has thousands of parts.
Even after the months-long job is finished, Dutschke isn't sure how long the organ will remain fungus-free. "We don't know how long the cleaning will keep, because we still don't really know what the reason for the mould is," he said.
The Evangelical Church in Central Germany (EKM) put the problem down to a combination of indoor air climate, excessive dust and the use of certain building materials and cleaning products. The organisation owns about 4,000 organs - nearly one for each of its churches.
EKM also fears that certain renovations, such as airtight windows and new heating systems - could be feeding the mould.
Church groups have launched an investigation to find out why their organs are such mould-magnets - and a number of foundations have also expressed interest in the project, which is expected to cost €260,000 and take up to three years.
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Meanwhile, Kares said one church organization had already found a solution to the mould problem: automated ventilation. He said the system, which opens and closes church windows based on air temperature and humidity levels, was both inexpensive and very effective.