Morrison abruptly exited the show on Friday, noting that he didn't 'follow competition production protocols.'
"Matthew was let go from SYTYCD after Fox did an internal investigation," the source says. "A female contestant received messages from Matthew on social media and felt uncomfortable about the tone. She brought this up to Fox executives who took it very seriously and after looking into it made the decision that Matthew crossed the line."
"Fox has provided the contestant with support and offered her any additional resources she may need," the source continues.
ET has reached out to both Morrison's reps and Fox for comment.
Per People, who was first to report the news, Morrison was fired from his judging gig on the dance competition series after an alleged "inappropriate relationship with a female contestant." A source close to the Fox reality show told People, "They didn't have sex, but he reached out to her through flirty direct messages on social media."
The source also noted that Morrison and the unidentified female contestant "never met up off-set."
"It was just messages that crossed the line," the source shared.
On Friday, the 43-year-old Morrison told Us Weekly that he was leaving due to not following "competition production protocols," though he did not elaborate.
"Having the opportunity to be a judge on So You Think You Can Dance was an incredible honor for me," the Glee alum said in a statement. "Therefore, it is my deepest regret to inform you that I will be leaving the show."
He added, "After filming the audition rounds for the show and completing the selection of the 12 finalists, I did not follow competition production protocols, preventing me from being able to judge the competition fairly. I cannot apologize enough to all involved and I will be watching alongside you all on what I know will be one of the best seasons yet."
It was just last month when a new panel of judges had been revealed for season 17 of the series, which included Morrison as well as Stephen "tWitch" Boss and JoJo Siwa. Longtime host Cat Deeley returned to emcee the new season.
Following news of Morrison's exit, Siwa clapped back at a troll on Twitter, who assumed she was the judge leaving SYTYCD. "Dammit. I saw the headline 'Judge Leaves #sytycd' and got all excited. Yes! @itsjojosiwa was out! But, nope. It was Matthew Morrison," the critic tweeted. "Dammit! I thought he brought the broadway perspective to the show. Maybe not an expert on dance, but on showmanship. Still won't watch."
Siwa retweeted the message on Tuesday, responding, "literally why tweet this?," before listing just a few of the accomplishments she has on her impressive resume.
"18 Years of Dance Knowledge, 4 Major dance TV shows, I’ve hired over 1000 dancers, 16 Dance music videos," Siwa boasted. "If you don’t like me that’s okay… but if you think I don’t know about dance ya just sound silly."
SYTYCD -- which premiered May 18 -- features dancers between 18 and 30 years of age showcasing their talents in various dance styles, including contemporary, tap, hip-hop, ballroom, animation, breaking and more. Those who are selected to move on to the SYTYCD studio will work with choreographers and compete each week in a variety of styles, with new twists introduced into the competition.