Police told Eyewitness News the woman appeared to be sleeping. Someone affiliated with Sacred Heart Cathedral called 911 and police began a death investigation.
The body is that of a white female - possibly in her 50s.
Detectives say they may know the woman's identity, but they were trying to make a positive ID.
Police spokesperson Jim Sughrue said it is not clear if the woman died at the church or if her body was taken there.
"That's the kind of thing that's under investigation at this point," Sughrue said. "As detectives learn more through the investigation we'll be able to share more with you."
Police confirmed it is a deceased person case.
"And until we learn otherwise, it will be treated as a homicide investigation," Sughrue said.
Tuesday's 12:30 mass was canceled along with a wedding, due to the investigation.
"The scene will be released as soon as it is possible to do that," Sughrue said. "But they will hold the scene until all the facts, all the evidence that can be gathered at the scene is, in fact, gathered."
Authorities removed the body about four hours after it was discovered. She was takento the medical examiner's office for an autopsy.
Police will release the woman's name after her family is notified.