Thomas, 23, is expected to front the AFLIU at league headquarters on Thursday, with his football career once again appearing in the balance.
"North Melbourne received notification from the AFL Integrity Unit on Wednesday that Tarryn Thomas is under investigation following a new allegation of inappropriate behaviour," the Kangaroos said in a statement.
"The club is working through this information and is not in a position to make any further comment."
AFL spokesperson Jay Allen confirmed the AFLIU are investigating.
Thomas was stood down by North Melbourne twice last year, first in February, then in March amid concerns over his behaviour towards women.
He was put through a respect and responsibility education program and spent three weeks in the VFL before later earning a senior recall, ultimately playing 12 AFL games last year.
In July, Thomas walked free from court without a criminal conviction for threatening to distribute intimate videos of his former partner.
He was initially charged with threatening to distribute an intimate image of another person, but this was downgraded by prosecutors to using a carriage service to harass someone.
Thomas was granted a diversion, which means he will escape a criminal conviction, and he was ordered to pay $1000 to charity.
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