The complaint concerned an incident that took place last Thursday and led to a hearing from Cricket Australia's Conduct Commissioner.
Four games into the 2022-23 season, the Thunder opted to immediately sever ties with Farooqi after the hearing and in a statement, said "all impacted parties have been offered support".
In a separate statement, Cricket Australia said it supported the decision to terminate Farooqi.
"The behaviours displayed by Fazalhaq Farooqi sit outside our values and it was determined that his contract be terminated," Cricket NSW chief executive Lee Germon said.
"Our focus now is providing the necessary support to those affected by this incident."
Cricket NSW declined to elaborate on the nature of the behavioural complaint when contacted by AAP.
The Thunder have yet to determine whether they will replace Farooqi, who was himself a replacement for platinum draft selection David Willey, the English left-arm quick who withdrew before the tournament began.
The latest incident continues a difficult start to the summer for the Thunder, who sit second-last on the ladder with only one win from four games.
The side was bowled out for the lowest total in professional men's T20 cricket - 15 runs - in their second game of the tournament by the Adelaide Strikers.
In the next game, the Thunder lost captain Jason Sangha to a collarbone injury that is likely to end his BBL campaign and are also missing highly-rated spinner Tanveer Sangha to a back injury.
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