Officers attended the incident at Doctors, on Forrest Road, on Saturday night after being called by bar staff, with one employee saying the women were “belligerent”.
The transgender employee, who identifies as they/she, also said that campaign leaflets against the reform of the Gender Recognition Act had been left in the pub’s toilets.
However, some of the women involved said they had been targeted by the employee in question who had described them as “hateful”.
Now Greene King, the chain which runs Doctors – and 19 other premises in Edinburgh – has launched an internal investigation and police enquiries are also continuing.
The row, which exploded on social media on Sunday, has seen the chain dragged into the angry debate over government proposals to change a law which would allow transgender people to alter the sex on their birth certificate without a medical diagnosis of gender dysphoria.
Some feminist groups claim that such a move undermines women’s rights, and removes protections from same-sex places such as refuges, hospital wards and prisons, which has seen them branded as “transphobic”.
According to one woman involved they were told by a staff member to leave the pub after they had eaten, claiming their booking time was up.
"I explained the booking email had no expiry time on it and asked why should we be made to move,” she said.
"She then told me that we needed to move and we should take the hateful stickers we had put in the bathroom with us.
"I told her I had not put a sticker anywhere. She accused me and my friends of being hateful and it was quite clear that a reason was being manufactured to get us to move.”
However on Twitter the employee said the police were called because “staff and other customers” felt “threatened.”
They added: “I should have kicked them out the minute they appeared. The whole bar team knew who they were from the start and asked me if I was comfortable with them.
“I decided… to try to diplomatically ease them out by using the two-hour per booking rule. They refused to budge.
“Some customers asked what was happening and I told them the same account I told the police. They were horrified but thankful for me dealing with it the way I'm trained.”
The woman involved said the police arrived around 10.35pm and added. "The officers spoke to several people, and one told me that everything we had told them would be in their report to the licensing board.”
A spokesperson for Doctors said they did not tolerate “any form of discrimination from our customers or teams” and added: "We are conducting an internal investigation and we will take appropriate action where necessary.”
A Police Scotland spokesperson said officers attended Doctors after a “report of a group of people refusing to leave a business premises” and added: “We have no reports of criminality at this time, but enquiries continue into the incident.”
This article was amended on 23 August to reflect the fact that the bar employee identifies as ‘they/she’.