Quarantine Tasmania head Danny Reardon said the investigation confirmed that two consignments of fruit had been mixed up by a fumigator in NSW.
The unfumigated shipment was sent to Tasmania with the certification for the other shipment.
Fruit fly larvae were found in one guava sold at Woolworths in Claremont late last month.
"Our investigation has not found evidence indicating a deliberate attempt by the fumigator not to comply with Tasmania's import requirements," he said.
"It has identified a number of inadequacies in the management and identification of the treated fruit, which we require to be corrected."
Mr Reardon said the corrections would need to be audited by Quarantine Tasmania and the NSW Department of Primary Industries before the company could be reaccredited.
He said the process would take months and would result in a significant financial penalty for the company.
Quarantine Tasmania also started the process to issue an infringement notice to importer Woolworths for two offences under quarantine laws.
Mr Reardon said Woolworths would be fined $1000 for importing non-fumigated material that required fumigation and $1000 for importing material that contained a prohibited pest.
He said he was confident the action taken would keep risks low, but called on the community to stay vigilant.
Liberal primary industries spokeswoman Sue Napier welcomed the actions and said it was important to send a strong message that breaches would be punished.