Australian Venue Company (AVC), which operates more than 200 pubs across the country, reportedly notified venue managers it would not celebrate Australia Day on January 26 because the day caused "hurt" and "sadness for some members of our community".
But in a statement this afternoon, AVC appeared to backtrack, acknowledging its comments caused "both concern and confusion".
"We sincerely regret that — our purpose is to reinforce community in our venues, not divide it," the statement read.
"It is not for us to tell anyone whether or how to celebrate Australia Day.
"We acknowledge that and we apologise for our comments.
"It certainly wasn't our intention to offend anyone."
It added that the company employed 9,600 people and welcomed about 15 million patrons each year.
"Across our community of team members and patrons, many different views are held and we acknowledge that," it said.
"Whether you choose to celebrate Australia Day or not, everyone is welcome in our pubs, always.
"We have been, and are always, open over Australia Day and we continue to book events for patrons."
Australian Hotels Association SA president David Basheer said the association did not advise or tell its members what to do regarding Australia Day, adding it was something "individual hotels had made their own decision" about.
"This is probably the first time we've seen it where hotels have come out and said, 'No, we actually don't want to celebrate the day,'" he told ABC Radio Adelaide.
The national public holiday has been rejected by some organisations and local governments due to the date it is celebrated, January 26, which some members of the Indigenous community say marks the day Britain colonised their land.
It is often referred to as "Invasion Day".
First Fleet arrived January 18
Britain's First Fleet of 11 ships arrived at Botany Bay on January 18, 1788, after sailing from England on May 13 the previous year.
The site had been chosen for settlement nearly 20 years earlier, in 1770, by Captain James Cook aboard the HMB Endeavour.
Upon landing, Captain Cook was challenged by two members of the Gweagal clan of the Dharawal people, who threw spears and rocks before they were shot at with muskets and one of them was wounded.