The spokesman said Jagger, 70, was "completely shocked and devastated" by the death of the 49-year-old Scott. US media reported that the former model was found hanged.
Jagger is currently in Australia, where he is touring with the Stones, who were due to perform in Perth on Wednesday.
Scott had dated the Rolling Stones frontman since 2001 following his split from wife Jerry Hall.
There had been no public sign that anything was wrong. The designer's official Twitter account was last updated with a link to a fashion shoot, after police were called to her apartment.
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"Heartbroken to learn of the loss of the lovely and talented L'Wren Scott. My thoughts and prayers are with her family. May she rest in peace," she wrote.
New York police refused to release any name but confirmed that officers found a dead woman at 200 11th Avenue in Manhattan's Chelsea neighborhood shortly after 10:00 am (1400 GMT).
"Upon arrival, officers discovered a 49-year-old female unconscious and unresponsive," a police spokeswoman told AFP.
"She was pronounced dead on arrival. The investigation is ongoing. The medical examiners will determine the cause of death."
A spokesman for the New York Fire Department confirmed only that firefighters had found a dead body when called to the address to respond to a "possible cardiac arrest."
US media reports said the six-foot, four-inch (1.93m) Scott was found with a scarf tied around her neck.
No note was found, local media reported.
Famous for her relationship with Jagger, Scott was also a hugely successful designer whose body-hugging and figure-flattering dresses were loved by Hollywood stars and Michelle Obama alike.
Only last month she had debuted her line at London Fashion Week.
In a relationship for well over a decade with Jagger, she had appeared to give the aging rocker a degree of romantic stability despite the couple's 21-year age gap.
He twice married models -- Bianca and Jerry Hall -- while other ex-lovers include singers Marianne Faithfull and Carla Bruni, who is now married to former French president Nicolas Sarkozy.