Two-thirds of employers are unaware members pay any charges in their defined contribution schemes, Department for Work and Pensions (DWP) research reveals.
A DWP survey of 719 trust-based schemes, 514 contract-based schemes and ten leading contract-based providers found employer awareness of member charges was "low".
Only 28% of trust-based and 33% of contract-based schemes believed that members themselves paid any charges at all.
There was even less awareness among small schemes - only 11% of trust-based schemes with six to 11 members and 21% of contract-based schemes in the same size category thought their members incurred any charges.
The report stated: "It is reasonable to conclude that there is low employer awareness of charges, as opposed to concluding that members are not paying charges: we know that members do pay charges in most cases."
The DWP said schemes with 100 members or more and those that used an adviser were far more likely to be aware of member charges.
The survey also found the average AMC was cheaper for trust-based schemes at 0.71% per annum, compared with contract-based schemes at 0.95%.
It found active member discounts were gaining popularity among contract-based schemes - with 16% of contract-based schemes using AMDs, compared to just 4% of trust-based schemes.
Some large providers claimed to have sold the majority of their contract-based schemes on this basis in the past 12 months as employers try to encourage employee retention.
Active member discounts have been criticised as "deferred member penalties" for imposing higher fees on members who stop contributing when they leave the company.
The findings will increase concerns that charges are too high and could undermine the introduction of auto-enrolment.
Earlier this year, Labour leader Ed Miliband raised fears of a mis-selling scandal if charges do not fall and floated the idea of a 0.5% benchmark.
Pensions minister Steve Webb said the government would not hesitate to impose a cap if necessary, but argued auto-enrolment was driving costs down.
The National Association of Pension Funds is set to publish the final version of its voluntary code of conduct on fees this autumn.
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