The survey of 100 charity pension scheme trustees and employers, revealed 70% were concerned about the current level of deficit, while a further 57% admitted to using charitable reserves to service it.
The survey states the results are a clear indication of the economic downturn's effect on the charity sector. It revealed over the last 12 months, liabilities for many organisations have run into millions of pounds, placing a significant strain on the sector.
This has been compounded by a general reduction in donation income, alongside funding cuts from the Government. This means charities are facing increasingly tough choices in order to reduce the deficit.
Mike Carpenter, director at Carpenter Rees, said: "It's no surprise to learn that as pension deficits rise to record levels, charities are having to decide how to balance their books.
"The current situation is symptomatic of a general downward cycle in gilt yield, which has been caused by the Government's need to pump capital into the financial markets.
"The impact on the charity sector has been brutal to say the least, so it's imperative that trustees and employers manage the pension fund deficit, or face the unwanted consequences - redundancy and administration."
According to the survey, the effect of the downturn is set to impact on employment on the charity sector, as 28% of respondents said they are looking at making redundancies within their organisation.
The survey also showed that while 71% of respondents said they are putting plans into place to deal with the deficit, 42% said they weren't confident in making informed decisions due to a general lack of knowledge.
Carpenter added: "There is a significant gap here in knowledge and action, which needs to be filled over the next few years as schemes try to deal with the deficit. Sadly, this makes for very sober reading when we consider the good work done by charities across the UK."
