Calvert Investments said on Tuesday it overstated the value of some of its mutual funds for several years and agreed to settle a civil case with the U.S. Securities and Exchange Commission after being accused of mispricing bonds and collecting inflated fees.Calvert said it would pay a $3.9 million penalty and reimburse affected shareholders as part of the settlement.

"The mistakes made in the past are regrettable and Calvert sincerely apologies for them," Calvert Chief Executive John Streur said in a statement. "Calvert has taken great steps to strengthen its policies and procedures."

Bethesda, Maryland-based Calvert, which manages about $12 billion, said it has overhauled its compliance department, separating that oversight function from the company's legal department. Calvert began making management changes at the end of 2014 and has since appointed an entirely new senior leadership team.

Between March 18, 2008 and Oct. 18, 2011, Calvert misvalued bonds that caused funds to have the wrong net asset value. As a result, performance figures were incorrect and Calvert collected inflated fees, the company said in a statement.

The case against Calvert centered on illiquid, or hard to price, bonds issued by Toll Road Investors Partnership II LP, according to the SEC. Calvert funds acquired Toll Road bonds with a principal amount of $1.2 billion.

Calvert relied heavily on a third-party analytical tool to value the bonds, but valued some of the securities at a price that was 65 percent higher than the price assigned to the same bonds by a major industry participant on the same day, the SEC said.

Calvert eventually discovered the problem with the analytical tool and in October 2011 marked down the value of the 2005B series of the Toll Road bonds by more than 50 percent, the SEC said.

As a result of the inflated bond prices, some investors in Calvert funds purchased shares at higher prices than they should have paid, and Calvert collected higher asset-based fees, the SEC said.

In December 2011, Calvert contributed $27 million to the Calvert funds affected by the mispricing. But the SEC said the process used was flawed.

Calvert said it is too early to determine the ultimate amount paid to affected shareholders as it reprocesses reimbursement amounts.

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