The "Tik Tok" hitmaker had appealed a decision in February that said she could not be released from her contract with producer Dr Luke.
Kesha has alleged that Dr Luke, whose real name is Lukasz Gottwald, had sexually, emotionally and physically abused her.
Dr Luke's record label is affiliated with Sony.
Manhattan state Supreme Court Justice Shirley Werner Kornreich noted that Kesha had "failed to plead that any of the alleged discrimination occurred in New York State or City," and that the court had no jurisdiction over the claims.
"Although Gottwald's alleged actions were directed to Kesha, who is female, (her claims) do not allege that Gottwald harbored animus toward women or was motivated by gender animus when he allegedly behaved violently toward Kesha," the judge wrote.
"Every rape is not a gender-motivated hate crime."
Moreover, the decision said that the statute of limitations on the claims had expired.
The case has attracted widespread interest, with many celebrities tweeting their support. Taylor Swift pledged to donate USD 250,000 to support Kesha.
Kesha, whose full name is Kesha Rose Sebert, alleged in a suit filed in Los Angeles in 2014 that Dr Luke, a powerful figure in pop music, persuaded her to move away from her family in Nashville at 18 to pursue a glamorous career as a pop star in 2005.
Gottwald brought the dispute cross-country by filing a lawsuit in New York Superior Court alleging defamation and breach of contract, claiming New York was the appropriate venue for claims related to their contracts.
The California court stayed Kesha's lawsuit pending resolution of the actions in New York, prompting the singer to file counterclaims alleging sexual harassment, gender-based violation and intentional infliction of emotional distress.
Kesha is seeking undisclosed monetary damages and to be let out of her contracts. She has asked to record outside the purview of Dr Luke, saying that as long as she's tied to the producer her career will suffer.
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