Federal independent MP Craig Thomson allegedly called escort services from a Melbourne hotel opposite the former Federal Court building, the jurisdiction that will hear the case against him.

Fair Work Australia has alleged that Mr Thomson, the member for Dobell on the central New South Wales coast, misused $102,337 in Health Services Union funds when he was the union's national secretary, including $5093 on escort services.

Pacific International Suites, now called Mantra on Little Bourke, from where he is alleged to have called escort services on two nights, is located opposite the building that housed the Federal Court from 1980 to 1999.

Federal Court documents allege, in the civil matter, that Mr Thomson withdrew $2200 using a Health Services Union Mastercard to spend on escort services in Melbourne or to replenish his cash supply after using those services in 2006.

In the first instance, on April 11, 2006, Mr Thomson is alleged to have used the HSU card to withdraw $500 cash from a Terrigal Beach ATM on the New South Wales coast. He is then alleged to have travelled from Sydney to Melbourne, via Brisbane, and withdrawn a further $300 from an ANZ ATM in Bourke Street.

In Melbourne, the documents allege, Mr Thomson called a Terrigal Beach number and then called the Boardroom in Melbourne, a brothel in Market Street, South Melbourne.

The Boardroom's website claims to have 62 escorts for hire and to be Australia's most awarded brothel and escort service.

Nine days later, Mr Thomson is alleged to have withdrawn $400 from a Cashcard machine at a Caltex service station in Forresters Beach on the NSW coast. Later that day, Mr Thomson flew from Sydney to Melbourne where he stayed in room 2004 at the Grand Hyatt hotel in Collins Street, after changing his flight to allow him to spend the night in Melbourne.

Documents allege he again called a Terrigal Beach number before calling the Young Blondes escort service and then the Confidential Model Escorts agency from the Grand Hyatt.

On June 6, the court documents claim, Mr Thomson withdrew $500 cash from an ANZ ATM in Caltex at Erina on the NSW coast and then flew to Melbourne from Sydney where he returned to Pacific International Suites. He is said to have stayed in room 613. On June 7 or 8, he withdrew more cash from a 7-11 store in Melbourne, again using the Mastercard.

On June 7, the documents allege, Mr Thomson called the Miss Behaving escort agency and used some or all of the cash from Erina and the 7-11 to pay for the service.

The documents allege Mr Thomson made 287 cash withdrawals from the HSU totalling $102,337.45, including cash advance charges. The documents claim 37 alleged breaches of rules for officers of registered organisations, such as unions, and 25 alleged breaches of HSU rules.

Mr Thomson has denied wrongdoing and has declared he is paying his own legal costs.

Proceedings against him in Melbourne will begin at the new Federal Court in William Street, a six-minute walk from the hotel where he is alleged to have used the cash to procure the escorts.