Monster, Keep Your Head Up and Breaking News all featured on the posthumous 2010 compilation album Michael.
They have since been the subject of a court case brought by a fan, who claims the vocals are by a session singer.
Sony Music and Jackson's estate said their removal from streaming sites had nothing to do with their authenticity.
In a statement, they described the action as "the simplest and best way to move beyond the conversation associated with these tracks once and for all".
The continued: "The focus remains where it belongs - on the exciting new and existing projects celebrating Michael Jackson's legacy", including the Broadway musical MJ and a recently-announced biopic.
"The album's remaining tracks remain available," the statement concluded. "Nothing should be read into this action concerning the authenticity of the tracks - it is just time to move beyond the distraction surrounding them."