Inspections conducted last month found that many of Bertha's cutterhead openings were clogged with dirt, and that seals around the machine's main bearing have been damaged and will need to be replaced.
In a Monday night news release, WSDOT officials said replacing the seals "is a complicated process" and will take months to complete.
Seattle Tunnel Partners, the contractor handling the dig, is working with Bertha's manufacturer to determine the best way to get access to the seals, according to WSDOT.
"They are looking at two ways to access the seal area: through the back of the machine or by drilling an access shaft from the surface in front of the machine," WSDOT said in its news release.
Last week, WSDOT spokesman Lars Erickson 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 last week.
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.
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.
In it's Monday news release, WSDOT said the tunnel contractor has "not shown any evidence that suggests the state or taxpayers will be responsible for cost overruns associated with these repairs."
Bertha's ongoing problems have reminded some of a similar saga. Boston's "Big Dig" was a three and a half mile tunnel project that made history as the nation's most expensive highway project. It dealt with a long list of construction delays and problems. Construction started in 1991 and was scheduled to be finished in 1998, but the project wasn't finished until 2007.
According to the Boston Globe, the Big Dig will end up costing $22 billion, including interest. That's a far cry from the original estimate of $2.8 billion dollars, and Massachusetts tax payers got socked with much of the cost.