The image of the activist holding a gun was also posted on her Instagram page, promoting her new song.
After criticism on social media, Nicki Minaj posted an apology to the estate of Malcolm X.
Known for his civil rights work with black communities in the US, Malcom X was assassinated 49 years ago this month.
“That was never the official artwork nor is this an official single. This is a conversation. Not a single,” Nicki Minaj wrote.
“I apologize to the Malcolm X estate if the meaning of the photo was misconstrued. I have nothing but respect [and] adoration for u.”
Nicki Minaj added that the artwork was in no way meant to “undermine his efforts and legacy”.
In a radio interview Nicki Minaj said that she wrote the song to empower women because there are too many songs that attack women.
“It was almost parallel in my opinion because he has this big gun ready to shoot,” the singer said to Hot 97’s Angie Martinez.
“I looked at it as this is one of the most memorable people in our history, in black history, who voiced his opinion no matter what, and I understand how my intent was overlooked and I definitely didn’t want to offend his family or his legacy.”
The song was made “to have fun” not “to be disrespectful”, she added.
In her online apology, Nicki Minaj, 31, expressed confusion over why people had been offended by the image.
“What seems to be the issue now?” the 31-year-old wrote.
She added: “I am in the video shooting [the song] and there happened to be an iconic photo of Malcolm X ready to do the same thing for what he believed in!”
The picture was deleted from Nicki Minaj’s Instagram account, but was still on her website on Friday morning.
The track will appear on Nicki Minaj’s next album and a compilation album featuring artists including Lil Wayne and Drake.
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