State Department of Transportation said inspections conducted last month found that many of the cutterhead openings were clogged with dirt, and that seals around Bertha's main bearing have been damaged and will need to be repaired or replaced.
"So when the openings in the cutterhead are plugged, it makes it very difficult for soil to come through. And that behaves exactly like an obstruction would," said WSDOT's Matt Preedy.
There was no immediate estimate of how long the repairs would take. Spokesman Lars Erickson declined to say whether DOT considers the damage to be a major setback.
He said the damage to the seals was not caused by the obstructions that stopped Bertha on Dec. 6.
On a conference call with reporters, Todd Trepanier, the state transportation department's administrator for the Alaskan Way Viaduct replacement program, said it was too soon to say what effect Bertha's problems would have on Bertha's price tag.
"Anything about costs would be speculation," he said.
Since then, the giant machine has only made four feet of forward progress, then was stopped again due to abnormally high temperatures in its cutter.
The machine named "Bertha" is only one-tenth of the way toward completing a 1.7-mile tunnel. The tunnel will carry Highway 99 traffic and allow the removal of the aging Alaskan Way Viaduct along the Seattle waterfront.
The total viaduct replacement is estimated to be a $3.1 billion project.
In 2009, the Legislature approved the tunnel replacement. But they included a provision in the law requiring Seattle to pay for any cost overruns. Legal experts have said enforcing that requirement would be difficult, noting that the language of the amendment was vague.
Transportation Secretary Lynn Peterson has noted that there's a $200 million risk-reserve fund for the tunnel. The tunnel project is supposed to be finished in late 2015.