Australian Federal Police officers executed a search warrant at Mr Thomson's home in Wamberal on the Central Coast on Wednesday as a result of the investigation involving four federal agencies.
"A joint agency investigation involving AFP, ABF, Home Affairs and AUSTRAC has resulted in the execution of search warrants in NSW and Queensland today," a federal police spokesperson said on Wednesday when asked to confirm the activity at Mr Thomson's address.
"This activity is part of an ongoing investigation into a syndicate allegedly defrauding the Australian government."
The spokesperson declined to provide any further detail on the investigation.
There is no suggestion it is linked to the historical fraud that ended Mr Thomson's political career.
A former federal MP for the seat of Dobell on the NSW Central Coast, Mr Thomson was convicted in 2014 for misuse of Health Services Union funds when he was the union's national secretary between 2002 and 2007.
The funds were spent on fine dining with his wife and sex workers - personal expenses not permitted by the union. He avoided serving time in jail but was fined $25,000.
The scandal resulted in Mr Thomson's suspension from the Labor Party in 2012 while he was a sitting MP.
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