There were estimated betting winnings in Australia and overseas of more than $2 million identified in connection with the alleged match-fixing ring, police said.
Deputy Commissioner Graham Ashton said it was the biggest case of alleged match-fixing in Australian sports history.
"This is the first case we've uncovered of this level of match-fixing in Australia,'' said Ashton, who warned that Australia was susceptible to international match fixing.
"Further match-fixing risks are imminent in Australia, partly because of localised overseas betting on Australian sporting events due to our favourable time zone,'' Ashton said.
"It is vital that we continue gathering intelligence to take preventative action to make it difficult for organised crime to infiltrate our sporting codes.
He added: ``We hope this sends the message that we're not a soft touch... we'll be onto it.''
The Southern Stars have played 21 matches this season for 16 losses and four draws, with their only win a 1-0 victory over top-placed club Northcote City last month.
Those arrested are expected to face match-fixing charges, which can attract a 10-year maximum penalty.
FFA CEO David Gallop welcomed the investigation relating to suspicious betting activity and welcomed the investigation by the Sports Integrity Intelligence Unit within the force.
"The integrity of football is paramount,'' said Gallop.
"We provided information to Victoria Police within 24 hours of receiving an alert from our international betting integrity monitoring agents Sportradar, who then worked closely with the investigation team.
"The arrests today show that the integrity measures put in place by FFA are working to detect illegal betting activity.
"We're determined to keep football clean. Alongside other sports bodies in Australia and globally, we must eradicate corrupt behaviour from sport.''
In addition to the criminal proceedings in Victoria, FFA will charge the people arrested today under FFA's National Code of Conduct.
They will face a range of sanctions including life bans from football which would apply worldwide.
-AAP