"The welfare of our patrons has always been a top priority and we are working extremely closely with Victoria Police to support them in every way we can in this investigation," Tennis Australia CEO Steve Wood told reporters in a news conference on Friday.
"We have stepped up security. More people are patrolling the areas and have been asked to be extra vigilant."
This is the second time in a week that the security at the Open has come under the spotlight after a brawl between rival Serb and Croat fans marred the opening day of the grand slam.
The alleged assault also took place that same Monday but was not made public until Friday.
A statement from Victoria Police said: "Police are investigating a reported indecent assault at the Tennis Centre on Monday, Jan. 15.
"Around 5pm, a young boy entered the male toilets inside the Rod Laver Arena when it is alleged a male entered the cubicle and touched him inappropriately.
"The boy's mother alerted security when the boy did not come out. A search was conducted inside the toilets, and the boy reappeared after around five minutes and told his mother what happened."
Wood defended the tournament's decision not to make news of the assault public for five days as "our hands have been tied by the ongoing police investigation".
Denying accusations of a cover-up, he said: "Like other members of the community we were deeply shocked by this incident."
UTMOST IMPORTANCE
"Security is the utmost importance to Tennis Australia and we take this as a very serious matter. We wanted to cooperate with the police investigation and we did not want to jeopardise in anyway the police investigation.
"We did not come out with the information before because we were asked not to.
"Everything that can be done is being done."
Wood added that fans should not fear coming to the Open in light of the incident.
"We've got adequate security and we've stepped up security. This is a family tournament and we want to look after our patrons who come here."
The alleged indecent assault is the second incident to overshadow the on-court action at the Australian Open this week.
On Monday, around 150 fans were evicted from the grounds after Serbs and Croats clashed on the grounds. Police admitted they had been unprepared to deal with the brawling fans.
Woods said the two events should not tarnish the image of the grand slam.
"We swiftly handled the other incident. Certain incidents like these bring us a few challenges but we are working through them.
"We have a great reputation around the world and we are known as the 'Happy Slam'".