Here’s a big media business story breaking today: The Street reports that Morgan Stanley Investment Management, a big investor in The New York Times Co., says it and others have withheld votes for the public corporation’s director nominees to challenge the Sulzberger family’s control of the company. MSIM made the charge today that the company’s board and management have become unaccountable to shareholders and claimed “other long-term institutional shareholders have also withheld their votes for the company’s Class A director nominees.” MSIM, which says it owns more than 5% of the Times’ Class A stock, called for the elimination of the dual-stock structure that leaves control of the board with minority shareholders led by the founding Sulzberger family.

“MSIM believes that the dual-class voting at The New York Times Co., which is an exception to the general rule of one-share, one-vote, creates special privileges as well as responsibilities,” the firm said in today’s statement out of London. “MSIM contends that the Board and management at The New York Times Co. have failed to fulfill these responsibilities effectively. While it may have at one time been designed to protect the editorial independence and the integrity of the news franchise, the dual-class voting structure now fosters a lack of accountability to all of the company’s shareholders.”

New York Times Co. stock has dropped 52% since its peak in June 2002, Morgan Stanley says. “As a long-term, committed shareholder since 1996, MSIM has privately conveyed its concerns to the company’s Board and senior management on a number of occasions and has suggested substantive strategies to operate the business better and allocate capital more efficiently. However, to date, the Board and management have failed to take the actions necessary to improve operational and financial performance.”

This has been happening more and more recently: Carl Icahn taking on Time Warner’s Dick Parsons (settlement), Roy Disney and Stanley Gold taking on Disney’s Michael Eisner (Eisner left), activists demanding a sale of Knight Ridder (surrender). The chairman of the family-owned New York Times Co. is Arthur O. “Pinch” Sulzberger, Jr., who became publisher of the NYT newspaper in 1992. A much-talked-about 2005 profile of Pinch by Ken Auletta in The New Yorker had as its central themes whether Sulzberger Jr. could handle himself in adversity and if he might even be fired. Forget the editorial missteps for a moment: the key is that operating profit is down and operating costs are up. But Auletta put a positive spin on Pinch’s future with this ending: “… his most important constituencies are the board and the family, and conversations with family members suggest that there is a united front. ‘The family rallies around Arthur in times like this,’ his cousin Dan Cohen said.” But now the challenge is coming from outside the family and against the family.