Angela Gibbins, head of global estates at the UK-based charity which promotes British culture and language around the world, reportedly attacked the young royal, then aged two, for his "white privilege" after a photograph was released to mark Queen Elizabeth II's 90th birthday earlier this year.
"White privilege. That cheeky grin is the innate knowledge he's royal, rich, advantaged and will never know ANY difficulties or hardships in life. Let's find photos of 3yo (year old) Syrian refugee children and see if they look alike, eh," Gibbins wrote on Facebook below one of the images of Prince George, The Sun reported.
British Council stressed that the comments do not reflect that of the charity.
A spokesperson said: "This comment was made on a private social media account. It has absolutely no connection to the British Council and does not represent the views of the British Council".
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"That said, we expect the highest standards of our staff and we will be investigating the matter further".
Prince George, who is third in line to Britain's throne after his grandfather Prince Charles and father Prince William, recently celebrated his third birthday on July 22.