The airport confirmed yesterday (Thursday) it submitted an application to the Civil Aviation Authority (CAA) for consideration.
It said it listened to feedback from communities and intends to deliver a “phased” approach in Spring 2018 and 2019.
This means new routes would be used only when needed and restricted to peak times (6am-10am), it said.
Last month 52 per cent of respondents to the second consultation were negative, with many concerned about noise, the consultation process and impact on communities.
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Edinburgh Airport Watch said: “We call on the airport to halt this flawed process now. The CAA must scrutinise this application very carefully, and understand that there is no community support for these changes.”
The flightpath over South Queensferry will not come into effect until 2019 and will be only flown over at peak times.
Alex-Cole Hamilton, MSP for Edinburgh West, said: “Whilst this is an improvement on the original proposals, we remain totally opposed to the inclusion of the airspace above South Queensferry in the redesign.
“South Queensferry was never part of the original design envelope so nobody from the Ferry participated in the original consultation.”
Chief executive of Edinburgh Airport, Gordon Dewar, said: “The listening exercise we embarked upon has been crucial to our thinking and we have altered our application following the feedback we received, demonstrating the importance of that public engagement.”
A final decision by the CAA is expected at the end of this year.