The music industry sent a wish list to Washington, but the response was not quite what it had expected.

Two years ago, Ascap and BMI, the industry’s two giant licensing clearinghouses, petitioned the Justice Department for changes to the regulatory agreements that have governed them since 1941. Those documents have not been changed in at least 15 years and, the agencies said, were in desperate need of updating to preserve the value of music in the digital age. The request came after both groups went through bruising litigation with Pandora Media over royalty rates.

But this week the government told the agencies it planned to deny their request, and added a twist that songwriters and industry executives say could further damage the economics of music and perhaps unsettle the business in fundamental ways.

In a meeting in Washington on Wednesday, Justice Department lawyers told representatives of Ascap and BMI that the two groups, called performing rights organizations, must adopt a policy known as “100 percent licensing,” which means that any party that controls a part of a composition can issue a license for the use of the whole thing. This went against decades of industry practice.