James Murdoch remains chairman of Sky despite a significant number of shareholders opposing his re-election.
Mr Murdoch survived the scare, which came from shareholders concerned about a potential conflict of interest as 21st Century Fox continues to pursue a deal for the piece of Sky it does not already own. Mr Murdoch is chief executive of Fox.
Shareholders took issue with Mr Murdoch, and with director pay at pay-TV company Sky's AGM on Wednesday.
"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.
Almost 22 percent of all shareholders opposed Mr Murdoch and 48.5 percent of independent shareholders.
Fox's US$15 billion bid for Sky is currently with UK competition watchdogs. Having been approved at an EU level and in other territories, it has faced numerous delays and hurdles in the UK.
The Sky AGM came as the company reported strong first quarter results, with 161,000 new customers and a 5 percent uptick in revenue of £3.3 billion. The company launched new streaming services in Spain and Switzerland in the quarter.
In terms of programming, Sky said Riviera became its most-watched original series ever in period, and Game of Thrones the most-watched series ever on Sky.