A statement released by the Coast Guard said human remains had been found overnight, dashing the hopes of family members who had been awaiting word on the six-member crew.
Although some human remains were found, they had not been identified.
Aboard the plane was a organ transplant team that included two doctors, two transport specialists and two pilots.
The team was returning from Milwaukee with unspecified organs for transplant to a patient in Michigan.
Soon after its departure, the plan declared an emergency and dropped off radar screens.
Within an hour, Coast Guard searchers locate what they believed is crash debris in Lake Michigan.
The cause of the crash is still under investigation.