Almost 45% of non-News Corporation shareholders failed to back James Murdoch as he was reappointed a director of BSkyB at the company's annual general meeting.
BSkyB said that excluding votes cast by News Corporation, Mr Murdoch received the support of 55.7% of independent shareholders, with 31.4% opposed and 12.9% withheld.
Mr Murdoch received the support of 75.4% of shareholders, with 17.4% opposed and 7.2% withheld.
There had been calls for the son of media tycoon Rupert Murdoch to resign his role as chairman amid fears that his links to the inquiry into phone hacking at News Corporation will damage BSkyB's reputation.
Deputy chairman Nicholas Ferguson said: "The board recognises that there have been contrasting views among shareholders on the question of the chairmanship. All shareholders have now had the opportunity to vote and we have a conclusive result. A clear majority, including a majority of independent shareholders, have voted for James Murdoch to continue in his role."
Protesters calling for Mr Murdoch's resignation gathered outside the meeting at the QEII conference centre in London.
Mr Ferguson took questions about Mr Murdoch's role and said: "He runs an excellent board. Discussions are open and frank, his chairing is very good. He has put in place strong governance procedures. He has a strong strategic view."
Mr Murdoch, who earlier this month faced tough questioning from MPs over reporting practices at the News of the World, has been BSkyB chairman for just under four years and recently resigned as director of News Group Newspapers, publisher of The Sun and The Times.
Labour MP Chris Bryant said: "It's a stark result for James Murdoch. I didn't anticipate the vote against him to be anywhere near as high. Only 1.7% of independent shareholders voted against him last year.
"He's got the rules, funds and family behind him - but I still think, as this row goes on, the writing's on the wall. I strongly suspect Sky will have dispensed with his services by this time next year."