Caroline Thomson, who is tipped to become the next BBC director general, said that attacks on the BBC by rival media groups, including the Murdochs, started to damage morale at the corporation "two or three years ago".
But she went on to suggest that past criticism, including a notorious speech by James Murdoch at the 2009 Edinburgh TV festival, appears rather hollow in light of the phone hacking scandal, which has seen the closure of the News of the World and arrests at sister paper The Sun.
In an interview with the Cumberland News, Thomson said: "Nothing is more important than the BBC's independence. You absolutely can't let politicians of any hue tell you what to do.
"Two or three years ago the level of negativity began to sap morale a bit. There was a lot of criticism from politicians and a lot of the press that are owned by people who are our competitors.
"Rupert Murdoch made a speech in which he lambasted Britain for having the BBC. James Murdoch said 'the only guarantor of independence is profit'. I think that looks a bit rich now."
In the 2009 MacTaggart lecture, James Murdoch accused the BBC of being overly dominant in the media industry, claiming that it was "dumping free, state-sponsored news on the market".
But last year, the BBC director general Mark Thompson hit back at the past criticism by James Murdoch, and also questioned the integrity of his father's News Corporation regarding the recent phone hacking scandal.
Caroline Thomson, who receives a pay package totalling £350,000 from the BBC, is considered among the leading candidates to replace Thompson when he steps down in the autumn.
She is one of the BBC's most powerful executives, particularly after taking on the role of deputy director general following the retirement of Mark Byford in March 2011.
Thomson told the Cumberland News that the opportunity to become the BBC's first female director general would be "enormously exciting".
"It's an enormous job. Mark Thompson once described it as like skateboarding downstairs holding a Ming vase," she said.
"If you've been as close to it as I have, you find the prospect that you might do it a bit awesome. You stop and think, my goodness, this would be big. On the other hand it would be enormously exciting and very challenging. So, we shall see."
Also in the interview, Thomson revealed that she got "death threats" three years ago over the BBC's refusal to broadcast a humanitarian appeal for Gaza following the Israeli invasion.
BBC bosses had pointed to the need for the corporation to maintain impartiality, but not everyone was convinced by that argument.
"I was on a train on the way up here [to Cumbria, where she has a home] for the weekend. I was rung up and told I'd got to go back and go on Newsnight and defend the decision," she said.
"Those things are quite tough. As well as tough questioning on the television, you get personal abuse. My emails completely collapsed. You get death threats.
"So there are times when it's not just scary because it's a big responsibility - it's actually scary."