He also claims her team have tried to extort him by threatening to "spread lies about him" unless he released her from her contract.
Kesha - real name Kesha Rose Serbert - also claims that the alleged abuse started early on when she signed her deal with the hitmaker, who is known for producing some of the biggest hits in pop music for the likes of Katy Perry and Britney Spears.
The suit also claims that Dr. Luke made "repeated sexual advances" towards her and "would use drugs and alcohol to remove her defences".
UsWeekly report that Kesha claims Dr. Luke allegedly gave her "sober pills" and the following day she woke up naked in his bed "sore and sick with no memory of how she got there".
After the alleged incident, Dr. Luke reportedly "threatened that if she ever mentioned the rape to anyone, he would shut her career down, take away all her publishing and recording rights, and otherwise destroy not only her life but her entire family's lives as well."
The lawsuit also alleges that he also "threatened her and her family's physical safety".
MailOnline has reached out to representative for both Kesha and Dr. Luke who have so far been unavailable for comment.
The news comes after Kesha was sent to rehab earlier this year for a reported eating disorder, which the lawsuit claims was caused by the abuse.
In April this year, TMZ reported that Dr. Luke was behind Kesha's eating disorder, after he had called her "fat".
A source told the publication that he had told her she "looks like a f***ing refrigerator" and Kesha was understandably affected by it.
Kesha has hinted at a fall out with the producer before when she told her Twitter followers that she never wanted to record or release their hit song Die Young, which was pulled from radio stations after the devastating Sandy Hook shooting in 2012.
In September last year, one of Kesha's fans set up a petition "Free Kesha" to help release the singer from Dr. Luke's management.
Singer Adam Lambert, Songwriters of the Year Max Martin and Lukasz 'Dr. Luke Gottwald and singer Ke$ha at the 28th Annual ASCAP Pop Music Awards, 2011. Photo / Getty Images
It followed reports that Kesha had hardly any creative control of her second album Warrior.
Meanwhile, Kesha's lawyer, Mark Geragos, told TMZ in a statement: "This lawsuit is a wholehearted effort by Kesha to regain control of her music career and her personal freedom after suffering for ten years as a victim of mental manipulation, emotional abuse and an instance of sexual assault at the hands of Dr. Luke."
Geragos added: "The facts presented in our lawsuit paint a picture of a man who is controlling and willing to commit horrible acts of abuse in an attempt to intimidate an impressionable, talented, young female artist into submission for his personal gain. Kesha is focused on moving her life and her career beyond this terrible time."
Dr. Luke has produced all of Kesha's big hits including, Tik Tok, We R Who We R and Your Love Is My Drug.
He has also produced hundreds of hits for other artists, including Roar, California Gurls and Teenage Dream by Katy Perry, as well as Till The World Ends and Hold It Against Me by Britney Spears.
He's also worked with Taio Cruz, B.o.B, Jessie J, Flo Rida, Miley Cyrus,T.I., Nicki Minaj, Juicy J, Rihanna and Shakira.
He was nominated for a Grammy Award for Producer of the Year at the 53rd Grammy Awards for his work on Katy Perry's Teenage Dream album.
Dr. Luke's biggest songs
Since U Been Gone - Kelly Clarkson
Wrecking Ball - Miley Cyrus
Tik Tok - Kesha
I Kissed A Girl - Katy Perry
Roar - Katy Perry
California Gurls - Katy Perry
Who Knew - Pink
Hold It Against Me - Britney Spears
Domino - Jessie J
Where Have You Been - Rihanna
About You Now - Sugababes
- Daily Mail