Rumours of the star's late arrival began after Glee cast member Dot Marie Jones, who plays Coach Beiste, tweeted: "Gonna be a long day!! Some ppl show up late and just throw a wrench in things. Not cool! I'd rather be an hour early (I was) than 5 minutes late!"
Lohan's publicist Steven Honig has now told E! Online that the reports of tardiness are not true and that the actress was in hair and make-up.
"The production team came to us and said that they wanted to start right after lunch, which was at two," he explained. "They wanted to begin with Lindsay at three, so that meant she had a lot of time where she wasn't doing anything.
"That's why people didn't see her. She was then in hair and make-up and began after lunch at three."
Lohan is making a guest appearance as herself in the season finale of the popular Fox show, alongside guests Perez Hilton and Rex Lee.
Honig also expressed his frustration, saying that Lohan was merely being criticised because of her troubled past.
"If there was a problem yesterday, I would have just said, 'No comment', however I can't ignore this because this is utter B.S," he added. "This is a classic example of people trying to bash Lindsay. She busted her ass yesterday and is back on set again today."
Lohan will appear on the third season finale of Glee on Tuesday, May 22 at 8/7c on Fox in the US.
The episode will air on Thursday, May 24 at 9pm on Sky1 in the UK.