AFL CEO Andrew Dillon says the sexual assault allegations from an incident involving multiple Sydney players are "deeply concerning" and raise "broader issues for our game and our responsibilities as a sport".

In a statement on Tuesday evening, Dillon's first public commentary since news of the alleged incident broke on Monday, the AFL CEO said the matter remains under police investigation, adding "it is important that the police process is allowed to run its course".

He said the AFL is "clear about the standards we expect and the values we stand for", adding "being clear about our standards also means being prepared to act when those standards are not met".

"The conduct and serious allegations regarding Sydney Swans players are deeply concerning," Dillon said.

"While the matter remains under police investigation, it raises broader issues for our game and our responsibilities as a sport.

"The woman who made the report to police is entitled to privacy and care, and that should be respected.

"It is important that the police process is allowed to run its course.

"Sexual assault allegations are serious, regardless of who is involved, what time of year it is, or what they may mean for a season.

"Our first question should not be what this means for a football club. It should be whether our actions match the standards we stand for and the community expects of us.

"As a sport, and as an industry, we are clear about the standards we expect and the values we stand for and the need to uphold them.

"Being clear about our standards also means being prepared to act when those standards are not met.

"Notwithstanding the ongoing police investigation, the AFL and the Sydney Swans will consider the broader conduct of the players as more information comes to light."

Dillon's message comes as the Swans board is set to meet to make decisions regarding the immediate future of the players involved in the alleged incident.

Swans coach Dean Cox addressed the wider playing group at Swans HQ on Tuesday, but the players at the centre of the investigation were not present at the club.

Club officials are meeting with those players off-site to establish the facts surrounding the incident, with decisions regarding their immediate futures to be made at a board meeting either later on Tuesday or Wednesday morning.

"Obviously extremely disappointed with what's happened, and understand the questions and we'll update as we gather more information," Cox said.

"We're working our way through everything with the AFL and the relevant parties and we'll update when we get more information."