Mark Thompson spoke out after it emerged that some scenes from Frozen Planet were filmed in a zoo in Europe.
The BBC was criticised for “fakery” after real location of filming was only disclosed on the corporation’s website and not during the broadcast.
Mr Thompson told MPs: “I do rather wonder whether this was about polar bears or Lord Leveson and other matters.”
Therese Coffey, an MP on the Culture, Media and Sport committee said she believed the footage of a polar bear giving birth to its cubs, supposedly deep under the Arctic ice cap, was “genuine”.
Coffey asked if series narrator Sir David Attenborough would re-record the documentary to make it clear that scenes from the wild were mixed with footage from a German zoo.
Mr Thompson responded: “Some years ago we asked the public whether they would prefer if there were ‘on air’ mentions – either captions or labels – and the overwhelming response was that they did not want us to do that.”
This emerged in 2001 after a rare hatchet fish was “reanimated” on the BBC series The Blue Planet, using computer effects after a real fish that programme makers had captured died.
Lord Patten, the BBC Trust’s chairman said the shots couldn’t have been taken in the wild as the mother polar bear would have killed either her cubs or the cameraman.
He said: “The alternative was either dead bears or dead people.”
He then added: “Out of almost eight million who watched the programme, 32 had raised an objection.”