SLC in a statement said ticket holders and fans could not get to their allocated seats at the Dambulla International Stadium due to the large numbers of people.
The statement said the stadium has a capacity of 18,000 while over 45,000 fans attended the match as per SLC security estimates.
SLC said the security staff and the ushering teams lost the crowd control systems which was in place to assist the spectators.
SLC officials said due to the situation contingency measures were taken to protect the playing area and the 2 teams.
SLC added all adequate measures will be taken to ensure that proper security and ushering will be in place for the upcoming matches and apologised to the public for the inconvenience caused to the fans.
Sri Lanka lost the 3rd ODI by two wickets with Australia taking a 2-1 lead.