A troubled insurance company owned by Warren Buffett’s Berkshire Hathaway has agreed to pay $3 million to settle allegations that it jacked up prices on unwitting customers.

Linda Lacewell, superintendent of the New York Department of Financial Services, settled with Applied Underwriters and five related companies over the sale of “misleading” worker’s compensation insurance packages that ended up costing business owners more than they bargained for, according to a consent agreement between the DFS and Applied.

“Today we are holding Applied Underwriters responsible for illegally operating outside of the Department’s oversight to sell a complex product to hundreds of New York small and medium-sized businesses,” Lacewell said in a statement.

Jeffrey Silver, Applied Underwriter’s general counsel, “expressed general satisfaction with the outcome,” the company said in a statement.

Applied, which Berkshire reportedly bought in 2016 for about $339 million, has been dogged by accusations from businesses and regulators that it skirts state limits on how much can be charged for worker’s compensation insurance — typically one of the biggest expenses for any small business.

Ex-customers have alleged in civil suits that its products are designed so that small businesses end up being responsible for covering the cost of their own insurance claims — a topsy-turvy arrangement they say amounts to a fraudulent “reverse Ponzi scheme.”

In a statement in April, Applied Underwriters said the worker’s comp package, called EquityComp, “is neither a reverse Ponzi scheme or a Ponzi scheme as alleged in court complaints.”

The company did not immediately return a request for comment on the New York agreement.

Regulators in California, Vermont and New Jersey have also clamped down on the Omaha-based company. California’s insurance regulator slammed the company for “bait and switch” tactics that pushed up the price of insurance.

After the New York DFS started its investigation in December 2015, Applied agreed to stop selling the insurance products in question, including “EquityComp” and “SolutionOne,” in the Empire State, according to the consent agreement.

“The program as implemented did not comply with New York law,” according to the settlement.

The Post first reported in April that the DFS was investigating Applied.

The settlement, which doesn’t require Applied or its officers to admit wrongdoing, helps clear the way for Berkshire to sell Applied, which it has said it is looking to do.

Last month, The Post reported on regulatory documents showing that Berkshire agreed to sell its stake to United Insurance Co., a Bahamas-based insurer, for an undisclosed amount.