A woman has been pushed over by a Protective Services Officer (PSO) during an arrest in the heart of Melbourne overnight.

Video shows the woman falling to the ground after being shoved by the officer outside Flinders Street Station about 1.30am.

Police said in the moments before the incident, plain clothed officers had been trying to apprehend a man and the woman ignored directions to stay back.

“A woman has tried to walk between police and the man they were trying to arrest. A PSO has pushed the woman, causing her to fall to the ground. She has then stood up and walked away from the scene,” the statement read.

“This incident is a timely reminder that arrests are dynamic and potentially dangerous situations. When police are responding to incidents, members of the public need to stand back to give police the space to ensure a safe and timely outcome for all parties.”

Video has emerged of the incident in Melbourne's CBD overnight. (Nine/Supplied)

The woman has not made a formal complaint, however Professional Standards Command has received a third-party complaint which will be probed.

Meanwhile, investigations are continuing into the sexual assault of a woman in the CBD in the early hours of Saturday morning.

Police believed six offenders approached two women on Queen Street about 3.55am, before stealing their tobacco and a speaker.

One of the victims was sexually assaulted, while the other was punched in the face.

Their attackers remain on the run.

One of the offenders is described as being African in appearance, aged in his late teens and wearing a white t-shirt with Balenciaga printed on the front.

Lord Mayor Sally Capp said the incidents were not linked to the nearby Moomba Festival “at all”.

“It’s unfortunately part of some of the normal activities that go during those hours in in the city,” she said.