That included votes cast on behalf of 21st Century Fox, Sky's largest shareholder, which is capped at 37.19% - and means that Mr Murdoch's appointment was also backed by a majority of independent shareholders.
James Murdoch has narrowly survived a rebellion by independent Sky shareholders to be re-elected as chair of the British satellite broadcaster.
The Murdoch family's Fox is trying to buy the 61 percent of Sky it does not already own.
Despite their position, Murdoch's level of support actually increased from 47% previous year, and the votes attached to Fox's 39% shareholding in Sky meant that both his reappointment and the remuneration report were approved comfortably overall.
Murdoch said at the Sky annual meeting that the companies were "engaged constructively with the regulatory authorities" about the deal.
Fox late previous year struck a deal to take full control of Sky.
"The board notes the significant vote against. the Directors' Remuneration Report, and. the re-election of James Murdoch, and will continue to engage with shareholders to understand their views as part of its ongoing programme of engagement", the company said on Thursday.
The shareholder, Hugh Lawson, said: "I think the board lacks independence".
In response to the question about the Fox News scandal, Darroch said the "whole board are incredibly supportive and behind Sky" and that it wanted to make a "broader contribution" to society.
Sharon White, Ofcom chief executive, has defended the decision made by the regulator over 21st Century Fox's proposed takeover of Sky.
The Competition and Markets Authority (CMA) has published an issues statement outlining the scope of its investigation into 21st Century Fox's planned ￡18.5 billion (€20.5 billion) takeover of Sky.
Like-for-like revenues during the three months to the end of September were £3.3bn, up 5.5% on the same period a year ago, while EBITDA (earnings before interest, taxation, depreciation and amortisation) rose by 11% to £582m.
"We've had a strong start to our new financial year with good revenue growth and excellent profit growth", said chief executive Jeremy Darroch.
European pay-TV giant Sky, facing a possible takeover by Rupert Murdoch´s 21st Century Fox, announced Thursday a surge in subscribers on keen demand for cult United States series Game of Thrones. The company launched new streaming services in Spain and Switzerland in the quarter.
Shares in 21st Century Fox were flat at $25.50 in light-volume trading.