The 73-year-old actor plays the wizard Gandalf in the Peter Jackson-directed film, a prequel to the Lord of the Rings trilogy.
He told ContactMusic that he became upset while filming a sequence on green screen with only visual aids to act against.
He said: "In order to shoot the dwarves and a large Gandalf, we couldn't be in the same set. All I had for company was 13 photographs of the dwarves on top of stands with little lights - whoever's talking flashes up.
"Pretending you're with 13 other people when you're on your own, it stretches your technical ability to the absolute limits.
"I cried, actually. I cried. Then I said out loud, 'This is not why I became an actor'. Unfortunately the microphone was on and the whole studio heard."
The first movie in the three-part Hobbit series, The Hobbit: An Unexpected Journey, is due for release on December 13 in the UK and US.
Watch a trailer for The Hobbit: An Unexpected Journey below: