The Pensions Trust was "bitterly disappointed" to discover its Pension Protection Fund levy had risen by £850,000 a year.
The body – which looks after the pensions of more than 4000 charitable, social, educational, voluntary and not-for-profit organisations – said it was dismayed its original estimate was so far off due to the increase in the scaling 1.16 from 3.77.
Head of customer relations Logan Anderson said: "We accept that the provisional figure carried a caveat, but we are dismayed that the PPF could get this so wrong.
"We have engaged with the PPF, Dun & Bradstreet and our participating employers to try to ensure that our clients are treated more fairly. Now we just have to hope that those efforts will, to some extent, mitigate the impact of this unforeseen increase in the levy scaling factor."
He added: "The additional risk-based levy for our three largest multi-employer schemes amounts to some £670,000.
"For these schemes in particular, the PPF levy is, to all intents and purposes, a charitable donation. The chances of 165 schemes which form the Scottish Federation of Housing Associations Pension Scheme and 700 funds making up the Social Housing Pension Scheme and 2600 separate charitable organisations all becoming insolvent in the same year is practically nil. This makes the announcement all the more galling.
"We wonder when the levy is going to stabilise so we can make sensible provision for it in our schemes’ funding plans. The current situation is simply unacceptable."
A PPF spokeswoman said: "Following our consultation with industry last year, we announced that D & B have introduced a special methodology for charities and non-commercial organisations that better reflects their unique characteristics. This means that - in general - charities should have improved failure scores.
"With this year’s levy scaling factor, we had to take account of the significant volatility seen in scheme risk during the last 12 months – and make sure that we still collect the £675m we said we need to collect. Back in November, we highlighted how the indicative scaling factor was likely to change significantly."
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