But it means permission to build the terminal, which could involve dredging deeper shipping channels and a surge in the number and size of vessels coming into Liverpool, may be refused.
Last night, Peel Ports, which is behind the plans to build the post-Panamax facility, insisted it would work with the Government and other agencies to try to hammer out a compromise that will allow the scheme to go ahead.
It wants the city to be able to handle the world’s biggest container ships, built to fit down the new, wider Panama Canal, which is due to open in 2014.
Plans to build huge windfarms in the Irish Sea may also have to be altered because of the new designation. Developing Merseyside into a “superport” and a hub for the low carbon economy have been identified as crucial economic drivers for the future.
The region’s inward investment agency, The Mersey Partnership, has labelled both as “transformational sectors” potentially capable of boosting the city region’s coffers.
Failing to get the post-Panamax facility or the know-how of building wind farms would be a massive blow to the region.
The Department for Environment Food and Rural Affairs announced that a 170,200-hectare area of Liverpool Bay would be made a Special Protection Area (SPA) in August.
It hopes making it an SPA will protect “internationally important” colonies of both the red-throated diver and the common scoter.
The UK must protect rare or vulnerable species of birds, under EU laws set out in the European Bird Directive.
No restrictions for the bay area have yet been drawn up, but the Sea Fisheries Commission, which is responsible for the UK’s inshore waters, will be running a consultation between interested parties to establish how the area is managed.
But, in a report by Natural England, the Government’s environment advisor, setting out why Liverpool Bay should be made an SPA, it warned new developments will only be allowed to go ahead if research shows they have “no adverse effect” on the wildlife.
Natural England added: “This greatly enhances the protection provided for SPAs compared with some other designations.”
The environment experts continued: “Both common scoters and red-throated divers are very sensitive to noise and visual disturbance. Movements of objects (such as boats, and wind turbine blades) and increases in noise can stop the birds from feeding or cause them to fly away.“Overwintering birds are particularly affected by disturbance as the weather conditions are harsh and they need to lay down fat reserves to use when they migrate to their breeding grounds.”
Liverpool Bay supports 3.5% of North West Europe’s common scoters and 5.4% of the national population of red-throated divers.
Although breeding birds fly to other locations, those that stay use the area for feeding.
Responding to the SPA announcement, a Peel Ports spokesman said: “We are working closely with the Government agencies and non-governmental organisations to ensure delivery of the River Terminal, taking into account all our environmental responsibilities.
“Significant progress is being made on site investigation work and we firmly believe the scheme will reinforce Liverpool’s position as a major UK container port.”
A Centrica spokesman said the Liverpool Bay SPA does not overlap where they have permission to build a windfarm and that it is in the “very early” stages of drawing up their plans.
Mark Knowles, TMP’s low carbon economy manager, said: “We commented on these proposals with our partners six months ago. Developers interested in expanding off shore wind capacity in the Irish Sea have all known this designation was in the pipeline and are drawing up their plans accordingly.”