In addition to the weaker latches which could fly open, the steel bonnets are too heavy for the Commodore's bonnet struts and can fall on mechanics while working on a car.
Holden said it was unaware of any reported incidents of bonnets flying open on the Commodore in Australia, but pointed to examples overseas.
"We can't quantify how many of these bonnets have been fitted but we believe it to be in the thousands," said Tony Weber, the head of the car industry lobby group, the Federal Chamber of Automotive Industries.
"Part of the problem is that there is no way of tracing these parts and they have been used on crash repairs for years."
The counterfeit bonnets fit approximately 80,000 new Holden Commodores sold since 2014.
Holden engineer Rowan Lal said: "We understood there were counterfeit parts on the market and we wanted to test them to see how they performed. To the untrained eye it's almost impossible to pick the difference between genuine and non-genuine."
He said the non-genuine bonnets had incorrect fastenings and critical components were made of weaker metal.
"These parts may look like they can do the job but they can't when it really counts," said Mr Lal.
The counterfeit or non-genuine bonnets cost about half as much as the genuine item ($350 versus $700).
The warning comes as more than 500,000 counterfeit automotive parts from China and the Middle East have been seized in the past 12 months.
The growing number of non-genuine and counterfeit parts has been traced back to the insurance industry, which has been finding new ways to cut crash repair costs.
Many insurers put in their disclaimers that non-genuine car parts are allowed to be fitted during a repair, but few policy holders check the detail.
"We need to educate people about the dangers because a large proportion of the population never consider this issue, they always go for the cheapest insurance premium," says Mr Weber.
The car industry also announced it has established a website to allow consumers to "dob in suppliers of bogus parts" and that information will be passed on to Australian Border Force.