The firm manages about $A18 billion in investments, but said the June performance of Newcrest and Regis Resources in its growth stocks trust had impacted overall trust performance for the month.
Newcrest fell 32% in June and Regis dropped 28.8% after the gold price fell to $US1200 an ounce.
The drop coincided with Newcrest shares hitting a nine-year low after the company announced expected write-downs of $A5-6 billion, while a series of analysts downgrades in the lead-up to that announcement also hurt the company's reputation, prompting a disclosure review.
"The downgrade to 2014 production guidance as well as the fall in the gold price raised significant uncertainty around the long term plans and timeline targets at some of the assets including Lihir being achieved," Perennial said in its June report last week.
"As a result of the price and volume downgrades we are no longer confident that the company can grow cashflows from current levels.
"Our valuation for Newcrest has fallen considerably to below $10 and hence we sold out of our position during the month.
"We maintain a position in Regis Resources given its superior cost position, management quality and return profile."
Newcrest, which also fell about 13% in May, already impacted the performance of the trust that month, but Perennial said at the time that it continued to see valuation upside.
As at January, Newcrest made up 3.3% of the trust and Perennial added to its position in the company in January and April.
The trust was worth $290 million at the end of June.