The company said late Wednesday in an annual regulatory filing that its flagship ESPN sports channel lost 3 million subscribers in the latest fiscal year, finishing with 92 million, according to estimates from Nielsen.

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ESPN’s declining viewer base — down 7 million subscribers in two years — is presenting owner Walt Disney Co. with tough choices.

The company said late Wednesday in an annual regulatory filing that its flagship ESPN sports channel lost 3 million subscribers in the latest fiscal year, finishing with 92 million, according to estimates from Nielsen. Other Disney networks also registered declines.

Disney stock fell 3 percent Friday, the most in three months, dragging down other media stocks in the first trading day after the regulatory filing.

If Disney, the world’s largest entertainment company, can’t halt or slow the decline at its flagship sports network, subscriber and advertising dollars will shrink and undermine the company’s single largest source of profit. ESPN is burdened by costly sports-rights contracts, such as for Monday Night Football, that make it crucial to increase revenue from viewers and advertisers. Other media companies, like Time Warner’s HBO and CBS, have responded to pay-TV audience losses by introducing Web-based services for consumers who don’t subscribe to cable or satellite.

“The trend is not ESPN’s friend in this case,” said Paul Sweeney, a Bloomberg Intelligence analyst. “With a large fixed cost consisting mainly of its billions in sports-rights fees, any weakness in revenue impacts margins immediately.”

With fewer customers, Disney will earn less from pay-TV partners such as Comcast and Dish Network, which pay fees to carry channels based on subscriber numbers. Wells Fargo Securities analyst Marci Ryvicker, in a note Friday, calculated that the loss in subscribers in Disney’s sports networks cost the company $700 million in fee revenue and $200 million in earnings before interest, taxes, depreciation and amortization.

At the same time, a stand-alone ESPN Internet channel, while opening the network to millions of potential viewers who don’t subscribe to pay TV, could hasten the unraveling of the cable bundle, threatening the network’s revenue and other company-owned outlets including the Disney Channel, ABC Family and A+E Networks.

ESPN has been the biggest profit contributor for Disney for years. It’s the largest piece of a cable-networks division that delivered $6.8 billion in operating profit in the last fiscal year, or 46 percent of the firm’s total.