The Labour MP launched the motion after a request from Iain Cornish, chief executive of the Yorkshire Building Society, and has the backing of at least 147 MPs, many of whom are from rival political parties.
Cryer argues that building societies’ share of the burden is disproportionate.
The mutual sector has to pay approximately £200m per year for each of the next three years – equivalent to 15% of the mutual sector’s pre-tax profits in 2007/08.
Building societies are being made to cover losses resulting from the failure of Bradford & Bingley, the Icelandic banks and London Scottish Bank despite no society ever having made a call on the FSCS or its predecessor schemes.
A spokesman for the Yorkshire said: “These charges are based on how much retail funding organisations have, and societies have a lot because they are prudent.
“We are being made to pay for the bad boys of the banking sector who have been involved in wholesale funding.”
He added that when building societies signed up to the FSCS scheme they did not imagine that high street banks would go bust on such a scale as has been the case, and believed the mechanism would be used to bail out smaller firms.
In her motion, Cryer stated: “The impact on building societies contrasts starkly with the banking sector where the FSCS levy is typically well below 5% of pre-tax profits.”
She believes the way the FSCS levy works at the moment is against the interests of societies’ savers and borrowers.
Cryer is calling on the government to introduce a more equitable scheme for funding the insurance of deposits held with failed banks.
Skipton Building Society’s pre-tax profits of £22.5m for 2008 represented a big fall from the £163.9m it saw in 2007. This was partly due to the mutual having to pay a levy of £16.3m to the FSCS.
Skipton’s profits were almost half what they would have been had the FSCS provision not been required.
The amount each society has to pay is calculated roughly according to their share of the savings market.
David Cutter, chief executive of Skipton, said: “I find it perverse that savers, who provide the bedrock for the funding of mortgages in this country, are being penalised to help correct fundamental imbalances in the wider economy.”
The Building Societies Association is supporting Cryer’s motion.
A spokeswoman for the association said: “It angers us that societies are having to pay when they have behaved much more prudently than institutions that are failing.
“This levy hits societies’ profits which is not fair as it is bound to have an adverse affect on their members.”
Norwich & Peterborough’s pre-tax profit for 2008 was £5.9m – after a £5.5m reduction for its FSCS levy – compared with £24.3m in 2007.
A spokeswoman for the FSCS said that societies were given the chance last year to opt out of being included in the same deposit class as banks.