Wall Street's self-regulator ordered three of the nation's biggest brokerages to pay more than $30 million in restitution to clients allegedly overcharged on mutual-fund sales.

The wealth-management units of Wells Fargo & Co., Raymond James Financial Inc. and LPL Financial Holdings Inc. failed to waive mutual-fund sales fees for certain retirement-plan customers and charitable organizations, the Financial Industry Regulatory Authority Inc. said Monday.

Wells Fargo will have to pay about $15 million, Raymond James $8.7 million, and LPL $6.3 million.

The restitution follows a similar order against Merrill Lynch last year. Finra ordered the Bank of America Corp. unit in June 2014 to pay an $8 million fine and $24.4 million in restitution to settle allegations that it improperly applied mutual-fund sales charges to certain accounts.

Mutual-fund companies provide sales-charge waivers for retirement plans to keep them in line with Employee Retirement Income Security Act rules that are designed to reduce conflicts of interest.

But the various waiver programs can be difficult to manage.

Wells Fargo, Raymond James and LPL don't have to pay a fine because the firms themselves discovered that the fees had been charged to its customers and they then reported the problem to Finra.

Still, the firms failed to adequately supervise the sale of mutual funds that offered sales charge waivers, Finra said.

"The firms unreasonably relied on financial advisors to waive charges for retirement and eligible charitable organization accounts, without providing them with critical information and training," the regulator said.

Finra's enforcement chief, Brad Bennett, said the regulator "is ordering meaningful restitution to adversely affected investors consistent with our commitment to ensure that mutual fund investors get the full benefit of available fee and expense reductions."

A spokesman for Raymond James said the firm "proactively initiated client refunds and self-reported the findings."

An LPL spokeswoman said the firm "has begun providing restitution to affected investors as well as implementing process changes to further protect investors for this issue in the future."

Wells Fargo declined to comment.

All three firms consented to the restitution without admitting nor denying Finra's charges.

Write to Matthias Rieker at matthias.rieker@wsj.com

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