The spokesman said Jagger was "completely shocked and devastated" by the death of the 49-year-old Scott. US media reported that she was found hanged.
Jagger, 70, is currently in Perth, Australia, where he is touring with the Stones, according to his official Twitter account.
Scott, an American former model, had dated the Rolling Stones frontman since 2001 following his split from wife Jerry Hall.
"He is completely shocked and devastated by the news," his spokesman said.
New York police confirmed that officers found a dead woman after being called to an apartment 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."
"We cannot release any more information before any proper family notification," the police spokeswoman said.
The US media said the six-foot, four-inch (1.93m) Scott was found hanging with a scarf around her neck.
No note was found, local media reported.