Earlier this week, MailOnline claimed Amal Alamuddin's mother, Baria, wished her daughter to be married within the relatively small Druze sect, reported BBC online.
Clooney, 53, said the report published by the tabloid had been "negligent" in "exploit(ing) religious differences where none exist".
"Freedom of speech can be an inconvenience to (his) private life. We have family members all over the world, and the idea that someone would inflame any part of that world for the sole reason of selling papers should be criminal," he wrote in an op-ed for USA Today.
"We only became aware of Mr Clooney's concerns this morning and have launched a full investigation. However, we accept Mr Clooney's assurance that the story is inaccurate and we apologise to him, Miss Amal Alamuddin and her mother, Baria, for any distress caused.
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"We have removed the article from our website and will be contacting Mr Clooney's representatives to discuss giving him the opportunity to set the record straight."
The 'Monuments Men' got engagement to Alamuddin, a London-based barrister, in April this year.