The New York Post claimed that Lohan "freaked out" over a scene which mocked her personal troubles and "disappeared".
She was alleged to have avoided rehearsals and ignored producers, telling them she had "walking pneumonia" and had gone to hospital on Sunday to get her lungs checked.
"Lindsay missed every meeting she had for the film, including script reads and wardrobe meetings," a source said.
"Then she missed her flight to Atlanta on Sunday to shoot the movie. The producers had been getting signs Friday that she was a mess, and would not be fit to work."
The report concluded that Lohan only returned to set when Dimension Films threatened legal action and sent a private jet to collect her.
A rep for Lohan said: "These stories are untrue, and she is willingly fulfilling all of her obligations."
Lohan will make her Scary Movie 5 cameo alongside Charlie Sheen.