"This is a personal and private matter for Katie and her family," Holmes's attorney Jonathan Wolfe told the magazine.
The last time Cruise and Holmes were seen together in public was back in February.
She was notably absent from his "Rock of Ages" premiere earlier this month.
TMZ reports that the couple did have a prenup. Their estimated net worth is around $275 million.
Cruise, 49, and Holmes, 33, wed in Italy in November 2006 and they have a 6-year-old daughter named Suri.
It was Holmes' first marriage. Cruise was previously married to Nicole Kidman, with whom he has two children, and Mimi Rogers.