The actor has been the face of the coffee brand since 2006 and is a member of its sustainability advisory board, which works to ensure Nespresso sources coffee from well-run and sustainable farms.
He said the news, brought to light by Channel 4's Dispatches, showed they "still have work to do".
"We knew it was a big project when it started seven years ago, and honestly I was surprised and saddened to see this story," said the Oscar-winner.
"Clearly this board and this company still have work to do – and that work will be done.
"I would hope that this reporter [Anthony Barnett] will continue to investigate these conditions and report accurately if they do not improve.
"The check and balance of good corporate responsibility lies not just with the company itself but also independent journalists like Mr Barnett to hold everyone's promise to account."
Clooney, who is a political and social activist alongside his wife Amal, also said: “Having grown up working on a tobacco farm from the time I was 12 I’m uniquely aware of the complex issues regarding farming and child labour.”
Nespresso, which prides itself on producing coffee beans ethically, said it will stop buying coffee from farms in some parts of Guatemala, which is the 10th largest coffee producer in the world.
The company also called the use of child labour “unacceptable” and said it had launched an investigation to identify the farms featured in the Dispatches footage. Read its full statement here.