In an interview with KOMO News, Peterson also said she is now "very skeptical" that the project will be completed on time.
Construction continues on some parts of the Alaskan Way Viaduct replacement project. But Bertha, the tunnel boring machine, still sits idle and broken - the subject of a growing battle between the contractor, Seattle Tunnel Partners and the state Department of Transportation.
STP claims the state is responsible for leaving a well casing in Bertha's path that originally brought tunnel construction to a halt last year. But the state has already turned down a request from STP for $125 million for the damage to Bertha and the delay.
Peterson says it's "pretty clear" that the blame for the problems rest with the tunnel contractor.
She says documents provided to STP before tunnel construction began mention the well-casing dozens of times and show its location in maps. Even STP's own online database clearly shows the well's location.
Secretary Peterson says under the contract it was STP's responsibility to remove it beforehand. Since they didn't, they're responsible for covering cost overruns, she said.
STP Project Manager Chris Dixon says the tunnel contractor expects to get Bertha repaired and digging again by next spring.
Seattle Tunnel Partners originally promised to have the project finished by January 2016 - now they're saying it will be done by November 2016.
But Secretary Peterson says she isn't certain they'll even make that date.
"I would say that at this point I am skeptical of the dates, and we are going to try and manage through this together in partnership to make sure that we can complete the project," she says.
Peterson says she won't be certain of anything until Bertha is repaired and operating.
STP plans to begin digging a pit to get to Bertha in May - and they don't expect to even begin repairing the world's largest boring machine until October.