But officials say the bylaws do not enable the agency to restrict the number of fishermen, or to recover the costs of regulating the Dee fishery area.
Brian Jones, of the Agency's Conservation and Ecology Department, said administration and enforcement of the bylaws cost around £50,000 a year.
He said: "It costs the tax payer a lot of money, and hundreds of people can descend on the cockle beds causing damage to the eco-system, which is protected under British and European laws.
"Afterwards we often have hundreds of empty cockle bags left on the beds, and have even had the situation where several of them got caught in the Port of Mostyn pilot boat's rudder and put it out of action for several days.