The now independent federal MP is charged with 154 counts of fraud, allegedly committed while he was national secretary of the Health Services Union.
Ms Roxon, chair of the privileges committee, said its inquiry would be suspended until the charges against Thomson were resolved.
"Since the referral the committee has been progressing the inquiry, although its work is not yet complete," she told parliament.
"The committee considers that the laying of criminal charges raises significant issues in terms of the operation of the sub-judice convention."
The committee had therefore decided to suspend its inquiry.
"The inquiry remains live and at the conclusion of judicial proceedings the committee will consider how it will proceed with the inquiry," Ms Roxon said.