The proposal to lengthen the runway by 600m would have opened up the possibility of flights to and from further afield destinations in Europe.
However it has been strongly opposed by local residents living around the airport in east Belfast.
Northern Ireland Environment Minister Edwin Poots has referred the application to the country's Planning Appeals Commission which will establish a public inquiry.
Ryanair Chief Executive Michael O'Leary has promised the airport he would introduce more services there if the runway was extended.
