The department said crews started drilling 5-foot wide shafts Tuesday in front of the machine known as Bertha.
The shafts should allow workers to remove a metal pipe in front of the machine and assess any other problems.
The machine ground to a halt on Dec. 6 after running into the 8-inch diameter pipe that had been left in the ground in 2002 after the department checked groundwater in the area.
Bertha is stopped about 60 feet underground and one-tenth of the way toward completing a 1.7-mile tunnel. It will carry Highway 99 traffic and allow the removal of the Alaskan Way Viaduct.