The Fiskville training centre's closure and clean up has contributed to a $65 million net loss for the CFA in the past financial year.
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The government attributed the "one-off" loss to Fiskville, which was used to train firefighters but was found to have been contaminated with cancer-causing chemicals.
The now-closed facility south of Ballan was the subject of a parliamentary inquiry. The deficit was contained in the CFA's annual report, which was tabled in Parliament on Thursday.
Emergency Services Minister James Merlino said closing the toxic training facility had created a one-off deficit in the CFA budget but said the government had invested $80.7 million to remediate the site.