The move by Kelly to examine BAA's proposals - for a 442ha site with a second runway and terminal at Stansted - at a central government level means the plans will go before a public inquiry next year.
BAA welcomed the move by the transport secretary.
"We are pleased the Secretary of State has acted swiftly and demonstrated their willingness to get on with the project," said BAA Stansted Generation 2 (G2) project director Roger Pellman.
"Earlier this year, BAA submitted nearly 40 separate planning applications in support of the G2 runway project following four years of detailed and comprehensive planning work to deliver a key milestone of the Government's Air Transport White Paper. We now confidently look forward to presenting our case in front of an independent inspector at the forthcoming planning inquiry.
"There are huge social and economic benefits to be enjoyed from the development of a second runway at Stansted for the East of England, London and for UKplc, and we are fully committed to maximising these opportunities for millions of air travellers while at the same time doing all we can to limit, avoid and mitigate against any environmental impacts."