The rapper, who made the comments on Bravo's Watch What Happens Live, said that she "heard that might not be Britney" featuring on the will.i.am track.
The 34-year-old 'Let Me Blow Ya Mind' singer continued: "That's what I heard, but you know, I don't know... it could be Britney. But I heard it wasn't."
Britney Spears's representative Jeff Raymond subsequently told TMZ that the claims were "absolute BS".
Watch Eve make the comments on Watch What Happens Live below (US only):
Raymond said: "Britney sang the song. will.i.am wanted her for this song and she sang on it."
The video for a remix of 'Scream & Shout' was released today, featuring Diddy, Lil Wayne, Hit-Boy and Waka Flocka Flame in a hip-hop re-working of the song.
Watch the new video for the 'Scream & Shout' remix below: