A spokesman for the agency said: "We will not be opening any of the beds for harvesting by the fishermen this year in Wirral. We are disappointed the numbers of larger cockles are low but we must protect these and the smaller, younger cockles so that we will hope-fully have good population next year.
"Although the fishermen will be disappointed by this decision, I am sure that they will appreciate the need to look to the future to develop a sustainable fishery.
It follows sweeps of cockle beds at Thurstaston and West Kirby by fishermen in recent years that have rapidly depleted stocks. The cockle beds in Wirral were closed last year to protect supplies.
The premium prices paid by shellfish processors meant hundreds of cocklers flocked to the lucrative sites during the summer months.
A ban was introduced last year after stocks rapidly depleted the summer before when hundreds of fisherman travelled to the borough to harvest the mud flats each day.
The beds were also closed in 1997 in the Dee Estuary when the cockles stocks were virtually wiped out.