Greater Manchester Police are now appealing for any witnesses or anyone with further information to get in touch.
Officers have been carrying out forensics and evidence searches within a cordon around a small section of the Major Street car park, between Aytoun Street and Minshull Street.
Workers on the nearby building site have told Manchester Evening News that they believe the woman was dragged into nearby bushes before being attacked.
Local residents said that a 'security guard who was working overnight heard screams and went out to see what has happening,' adding: "The security guard found the woman and brought her into the reception to sit here down and help her".
It is thought the attacker had already left the scene by the time the security guard had come out to help.
Two PCSOs have been guarding the scene as people flooded into the city centre this morning with many stopping to ask what had happened.
Police officers were also patrolling the area, which is a short walk from both Piccadilly Gardens, and the top end of Canal Street and the Gay Village.
Later on this morning detectives were seen inside the cordon, talking and combing the area for clues.
Some wearing gloves seen picking up items from the floor, dusting them off and placing them in evidence bags.