It wasn't clear where they died or how, Columbia Police Chief Dean Crisp said.
The woman's apartment, a few hundred yards from where the bodies were found, was roped off, and investigators were looking at a possible domestic dispute, said police spokeswoman Sgt. Florence McCants.
"What we're doing now is working it in reverse," McCants said.
The woman's identity and the genders of the other two victims were not immediately released.
Richland County Coroner Gary Watts said authorities initially had difficulty reaching the bodies. By midmorning, the bodies had been removed from the pipe, which is larger than 3 feet in diameter, and were being taken to the coroner's office for identification, Crisp said.
"When you find a crime like this, it's clearly out of the ordinary," Crisp said.
Authorities had no suspects, he said.
A resident of the apartment complex reported seeing the bodies around 5 a.m., police Sgt. Florence McCants said. Police also received a call about gunshots in the area, but Crisp was unsure if it was related.
Dozens of complex residents gathered in small groups outside the crime scene tape. Authorities put tarps on a fence to shield the area from onlookers.
At the complex of one-story apartments, resident Tanyetta Brown said there had been recent crimes in the area.
"It's not that the neighborhood is dangerous, it's the company that you keep," Brown said.
Residents also expressed frustration about a lack of police presence in the area.
"You call the police and it takes three and four hours for them to get to a call," said Dorothy Ball, 75, who has lived at the complex for 18 years. "They don't patrol out here like they should. It makes me mad. It's terrible out here."
The complex is less than five miles from the state Capitol.