New South Wales Waratahs back rower Jacques Potgieter has been fined $20,000 by the Australian Rugby Union (ARU) for making homophobic comments during the side's Super Rugby clash with the Brumbies.

Brumbies flanker David Pocock twice complained to referee Craig Joubert on Sunday during the Brumbies' 28-13 loss on Sunday.

Potgieter admitted he made comments that are not in line with the inclusion policy endorsed by the ARU last year, designed to stop discrimination in the sport.

"We take the issue of homophobia in sport seriously and want to provide a positive environment for everyone involved in Rugby. Comments of this nature cannot be tolerated," ARU chief executive Bill Pulver said.

"Our inclusion policy reinforces Australian Rugby's commitment to ensure every individual, whether they're players, supporters, coaches or administrators, feel safe, welcome and included regardless of race, gender or sexuality.

"I'd like to stress again that there is absolutely no place for homophobia or any form of discrimination in our game and our actions and words on and off the field must reflect that."

SANZAR told the Brumbies immediately after the game that it was looking into the complaints and, after completing the preliminary investigation, handed the reins over to the ARU on Monday afternoon.

Shortly afterwards the ARU announced it had fined the South African $20,000, with half of it suspended.

Potgieter apologises for thoughtless remark

Potgieter will undergo educational and awareness training.

"I'm very sorry for any offence caused by what I said on the field during a heated encounter," he said in a Waratahs statement.

"It was an off-hand remark made without thought for the hurt it could cause to those around me."

Waratahs chief executive Greg Harris said the team had gone to great lengths to ensure it had an inclusive culture and Potgieter had "made an error in judgement".

"Our players have been educated around the importance of respect and integrity on the field, and this incident was directly in conflict to these values," Harris said.

"There is no place for homophobia or any form of discrimination in our game and we have endeavoured as a club to embody these values on and off the field.

"We pride ourselves on a strong culture, and this incident is by no means definitive of our collective identity as a football club."