A MELBOURNE court has fined Essendon $200,000 for bypassing medical staff and ignoring protocols when running its controversial supplements program.

The penalty follows guilty pleas by the club to two charges brought by WorkSafe Victoria for failing to provide and maintain a safe workplace in late 2011 and 2012, when players were being put through the controversial supplements regime.

Regardless of whether the players were given illegal substances or not, the club failed to follow its own procedures established in January 2012 after concerns were first raised about what players were being injected with, according to court documents.

Melbourne Magistrate Peter Reardon said the Bombers seemed to turn a blind eye to what was happening, and the club's conduct was a serious departure from its own protocols.

"Here we have head coach James Hird saying, 'go for it', but did he follow up?" Mr Reardon asked.

The safety breaches involved the invasion of the players' bodies via injections, he said.

There was no medical oversight and the whole thing was conducted under the cloak of secrecy, as players were told not to discuss the program to retain their competitive edge.

"It is impossible to tell how many injections the players were given and what was in them," the magistrate said.

The club was well-resourced and could have easily provided a safe place for the 34 players, he said.

"It did not. It did the opposite."

Garry Livermore, for Essendon, had previously submitted that a fine between $20,000 and $40,000 was appropriate because the club had already incurred significant penalties.

In August 2013 Essendon was kicked out of the finals series, fined $2 million and stripped of draft picks.

Twelve current players have been banned from the 2016 season for doping after the Court of Arbitration for Sport upheld an appeal against the decision to clear 34 players of taking a banned substance.

Mr Livermore told the Melbourne Magistrates Court at a previous hearing that Essendon had been co-operative with WorkSafe and was genuinely remorseful.

"There's no evidence any player was given a harmful substance or has suffered any harm," Mr Livermore said.

However, WorkSafe said this was because of poor record-keeping.

Prosecutor Ross Ray QC argued the number of players put at risk by the club's conduct was an aggravating factor.

The power imbalance between the club and the youth and vulnerability of some of the players should also be taken into consideration, he said.

Mr Reardon said it was hard to imagine players standing up to Hird, given his prestige.

He fined the club a total of $200,000 on Thursday and ordered it to pay WorkSafe's costs at $20,000.

Late on Thursday afternoon, the Bombers released a statement regarding the hearing.

"We understand this is a very serious matter and take responsibility for the governance failings of the club during 2011-2012," chairman Lindsay Tanner said.



"We are a vastly different Essendon Football Club compared to 2012, and we have implemented significant governance, compliance and integrity reforms across our organisation."