A team of up to 40 specialists is working through the night over 14 months to carry out the job, which is claimed will ensure there is no disruption to rail services on one of Scotland's busiest routes as work begins.
The site above the tunnels will be home to The Haymarket, a £200m development of shops, offices and hotels, with an underground car park being developed by Edinburgh Haymarket Developments. The project is a joint venture between Interserve, an international support services and construction group, and developers Tiger Developments.
It is one of Edinburgh's biggest commercial projects of the last ten years and is expected to create around 3,500 jobs.
David Westwater, Interserve development director, said the preparatory work is the main challenge before construction can begin above ground.
"It will be early next year before we can do that, but then people will soon start to see the development taking shape.
"After such a long time as a gap site, we're very excited about what The Haymarket has to offer and how it will help to create a real gateway at Edinburgh's west end."
The strengthening works will allow contractors to begin building the foundations for the development.
This includes water-proofing between the tunnel lining and the surrounding ground, and drilling and inserting metal bars within the brick lining.
Currently, engineers are only able to work in the north tunnel from midnight till 5am four nights a week and in the south tunnel from 1am to 9.30am for one night a week.
Proposals include four office buildings, shops, bars, cafes and restaurants.