Police Media confirmed the two men were charged and remanded with no further details available.
UP to 15 bikies stormed a Ballarat nightclub assaulting and intimidating staff and patrons early Saturday morning.
However, on Monday police attacked back, raiding seven premises across the region and arresting two men, believed to members of the outlaw Finks Motorcycle Gang.
One of the premises raided by police is believed to be the club's Ballarat clubhouse located in the CBD, only metres off Doveton Street North.
Ballarat Police Superintendent Andrew Allen said it was important for police to send a clear message to the motorcycle club.
"We know that the Finks are trying to establish themselves up here and if this is their attempt to try and muscle in and establish themselves as an outlaw motorcycle gang chapter in Ballarat, we will be there to arrest them, take them into custody and put them before the courts," he said.
"They might think they are making a statement on behalf of a criminal enterprise, however, we will respond and act accordingly and make sure all of those offenders are tracked down, arrested and brought before the courts."
The club is believed to have arrived in Ballarat around 18 months ago.
Superintendent Allen said Ballarat's two other outlaw motorcycle clubs, The Vikings and Bandidos, had not caused police too much grief in the past.
Two men are now in police custody as a result of the search warrants, with a loaded handgun also being found at one of the homes.
Superintendent Allen said the incident on Saturday morning was "an endeavour to standover and put fear into patrons and staff of the licensed premises".
The licensed premises where the assaults and robbery took place is believed to be the Haida Bar in Camp Street.
"What we are alleging is that a number of men, we believe most of those men belong to the outlaw Finks Motorcycle Gang, forced their way into the licensed premises on Camp Street, assaulted a number of staff and patrons, stole money from the premises and caused an affray inside those premises," Superintendent Allen.
The imposing police vehicle which rumbled into town today did more than deliver the state's elite police squad, the Special Operations Group.
It sent a very clear message.
The 'BearCat' armoured vehicle - all eight-and-a-half-tonnes of it - stood like an intimidating sentinel outside the entrance to Grainery Lane while police raided the Fink's Ballarat CBD clubhouse.
Two alleged bikies were arrested soon afterwards in locations around the Ballarat region after a robbery and assault inside a Ballarat nightclub on Saturday night.
Watch this Channel 7 report on the introduction of 'BearCat's to NSW Police last year:
Two men believed to be Finks Outlaw Motorcycle Club members were arrested this morning following an alleged robbery and affray at Haida Nightclub in Camp Street on Saturday night.
A number of search warrants were executed at the Finks clubhouse in Grainery Lane in the CBD and at two residential addresses in Smythes Creek and Wendouree West
The men are currently assisting police with their inquiries.
The warrants were executed after staff members and patrons at the camp street premises were assaulted and the venue was robbed shortly after midnight on Saturday morning.
Ballarat resident Michael Porter was on his regular morning walk with his wife when he noticed flashing lights on Sturt Street.
"There were a number of plain-clothed police officers, then we saw the big SWAT van," he said
"We heard over a speaker 'all occupants come out with your hands empty and visible'.
"Then there were two big explosions."
"All occupants come out with your hands empty and visible"Police over a loudspeaker this morning
Heavily armed police have raided a property in Ballarat's central business district this morning.
Police arrived in a black armored vehicle in Doveton Street just before 8am and also had a strong presence in Armstrong street.
Their focus was on Grainery Lane, between the two streets, the location of a property owned by The Finks Outlaw Motorcycle Club.
A steel door could be seen ripped from its hinges down Grainery Lane and police had both Armstrong Street and Doveton Street blocked to traffic for about 40 minutes.
The Finks do not have a permanent clubhouse in Ballarat, but are believed to visit this property intermittently.
In September 2011, large numbers of Finks members attended the CBD location for a gathering.
Ballarat police kept a close eye on the visitors that night, stating it was the first time there had been "any activity" from the group in Ballarat.
As part of that operation, a Victoria Police marked camera van was parked for extended periods in the northbound lane of Doveton Street, with a clear view down Grainery Lane.
Men wearing colours and insignia representing the Finks Motorcycle Club and its supporter groups were seen coming and going from a red-brick building in Grainery Lane during the day and into the night.
Several men bearing the club's insignia also stood at the entrance to Grainery Lane for much of the night.
The Finks were also spotted in Ballarat on November 28 last year, Finks members in full colours were spoken to by members of Ballarat Highway Patrol in Dana Street at about 1.30pm.
Members from Ballarat police uniform branch were also in attendance.
Police told The Courier those checks were simply routine and some "minor traffic infringements" were issued as a result.
It has been revealed recently that members of the Finks nationwide are being "patched over" by US based club The Mongols, the self proclaimed "baddest bikie gang in the world".
It has also been reported that The Mongols are "enemies" of the Hells Angels.
Two outlaw motorcycle clubs have clubhouses in Ballarat, the Vikings and Bandidos.
Neither club has been aligned to The Finks in the past.