Lukaku featured in a video on the Everton website saying there did not have to be "such a big deal" made about the gesture and that Anelka should not be banned. The video was later whipped off the website.
In a statement released through anti-discrimination group Kick It Out, for whom Lukaku is an ambassador, the forward apologised.
Lukaku said: "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."
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