Last winter, large parts of the Levels were deluged with flooding, leaving a village cut off for two months and a trunk road closed for several weeks.
Somerset County Council leader John Osman said the project would normally take two years to plan but this had been narrowed down to two months.
The road to Muchelney will be raised and culverts will go under the A372.
Muchelney has been cut off by flood water for some period of time each winter for the past two years.
During last winter's floods (December 2013 - February 2014 ) the village was cut off for two months, while the previous winter it was cut off for several days.
The plans are part of the 20-year Flood Action Plan with the council hoping it will secure access in future floods.
The work on the A372, which is a main route across the Somerset Levels, will take place at Beer Wall.
John Rowlands of the Environment Agency, which is also involved in the project, said: "At Beer Wall, the water course that runs underneath it is locally known as a the River Sowy.
"It's other name, rather fetchingly, is the Parrett Flood-Relief Channel - in other words it takes water from the River Parrett puts it into River Sowy, eventually into the King Sedgemoor's Drain and back out into the River Parrett at Dunball.
"What we're hoping to do with these works is to remove any constrictions that allow this channel to run at its maximum capacity."
The River Sowy will also be widened so Aller Moor can drain more quickly, to cut the flood risk.
A 547 yard-stretch (500m) of Drayton Road, which leads to Muchelney, will be raised by more than 3.9 ft (120 cm) at its lowest point.
Both projects will take up to 11 weeks to complete and road closures will be put in place.
Work has begun on two roads on the Somerset Levels in an effort to prevent communities being cut off by flooding.