Affleck, 42, and Garner, 43, announced their breakup last month after being together for a decade, reported E!Online.
"The story is complete garbage and full of lies. You shouldn't be able to hide behind 'blind sources' and attempt to destroy families going through a difficult time... It's shameful and desperate," a rep of the actor said.
There were reports that the Oscar-winning actor was seeing Christine, 28, a woman he and Jennifer hired as a nanny for their three children-Violet Affleck, nine, Seraphina Affleck, six, and Samuel Affleck, three, earlier this spring.