A high-profile investor in the New York Times Co. withheld votes for directors at the company’s annual meeting Tuesday in protest of the Times’ dual-class share structure.

Like several other publicly held newspaper publishers, the Times is still effectively controlled by descendants of its founding family — in its case, the Sulzbergers — through special shares of stock.

Morgan Stanley Investment Management Ltd., which owns about 5.6% of the company’s stock, said it withheld its votes for the four directors that are elected by the company’s Class A shares.

In a statement, Morgan Stanley Investment Management said it was calling for the elimination of the two-class shareholder structure, which it says disfavors public shareholders even though they own 99% of the company. A Times spokeswoman didn’t return calls seeking comment.

The fund noted that despite a 52% tumble in the company’s share price since its peak in June 2002, the compensation for the Times’ managers is “substantial” and has “increased considerably over this period.”