During an interview over the weekend, the 20-year-old suggested that the controversial gesture, which is seen as anti-semitic, was "not such a big deal".
The West Bromwich Albion striker was charged by the Football Association this week for making the gesture after scoring against West Ham United in December.
Lukaku said in a statement: "I want to make clear that I was supporting a friend and player I have admired since I was a child. I apologise if I caused any offence with my comments as this was never my intention.
"There has been a misunderstanding and I want to clarify that I was in no way endorsing the gesture made by Nicolas. I am proud to be a 'Next 20' ambassador for Kick It Out and will continue to inform young people of the harmful effects discrimination of any kind can have."
Reports emerged this morning claiming that the anti-racism group could drop Lukaku from his ambassadorial rule as a result of his comments.