"But a small minority of repeat toll evaders decline to use the range of payment options available to them and are flouting the law," he said.
"This is a situation that cannot be allowed to continue."
At the end of last month, a total of $717,983 was owed in unpaid tolls.
Mr Thackwray said the prosecutions were the "right thing to do" because it sent a message to other toll evaders and was in the interest of fairness for the vast majority of drivers who use the road and paid their tolls on time.
Automobile Association spokesman Simon Lambourne said it welcomed the action taken by the Transport Agency.
"Those motorists rorting the system are about to get a very clear message that their behaviour is unacceptable," Mr Lambourne said.
"These prosecutions are welcomed by all the law-abiding motorists who do pay their tolls."
At the start of the month, the toll was raised by 20c for cars and motorcyclists to accommodate for the higher running costs since the route opened, and for inflation and the GST increase.
Those who failed to pay within 28 days of receiving toll notices already face $40 infringement fines and, as of August last year, late transactions were increased from $2.20 to $4.90.
Charging motorists tolls to use the way is a means of repaying the $158 million the Transport Agency borrowed to build the route which had a $372.5 million total construction cost.
At the end of December, the agency had repaid $17.5 million.
UNPAID FINES
* Debtor 1 $2980
* Debtor 2$2280
* Debtor 3$1630
* Debtor 4 $1270
* Debtor 5 $1260.