Yakima has spent more than $300,000 in legal fees over the past year to make a case against a consulting firm that the city alleges botched part of the Lincoln Avenue underpass.

The city’s outside lawyers argue that the Federal Way firm should pay for millions of dollars in cost overruns that resulted from bad decisions on a critical piece of the project.

The city’s legal costs — which don’t include city staff time and other internal costs — likely will only grow before any resolution in the dispute, which is scheduled for trial next summer.

Yakima filed a lawsuit against the consulting firm, BergerABAM, last December, accusing it of negligence and incompetence in its work on the project’s designs.

Begun in 2010, the Lincoln underpass was completed in 2012, several months late and about $4 million over budget. The problems stemmed largely from the bottom of the trench built to separate the street from railroad tracks now overhead.

BergerABAM performed soil testing and helped draft bid requirements for the project, including specifications for constructing the bottom seal of the underpass. That bottom seal had to keep water out, support the railroad tracks overhead and resist the pressure of groundwater trying to push the entire trench up out of the ground.

The project contractor was allowed to choose between two construction methods. The contractor, Apollo Inc. of Kennewick, and the subcontractor, Geo Grout Inc. of San Francisco, chose the older and cheaper method called permeation grouting. In that technique, a liquid is injected into the soil, permeating the empty space in the soil and locking it together.

However, the work quickly ran into trouble, and had to be shut down in November 2010. Work resumed three months later, this time using a different technique: sinking concrete shafts 15 to 18 feet into the ground.

The concrete shaft method is being used on the Martin Luther King Jr. Boulevard underpass, currently under construction and on schedule to open in mid-2014.

The two underpasses are projected to cost about $41 million, coming largely from state and federal funding.

The city alleges BergerABAM didn’t take enough ground samples, took samples in the wrong places and ignored a subcontractor’s recommendation against allowing permeation grouting, among other accusations.

“I don’t think the taxpayers should have to pay for their lesson,” City Manager Tony O’Rourke said Friday.

The company denies the city’s claims, which it calls in court documents a “self-serving narrative.”

BergerABAM did not respond to a request for comment Friday afternoon.

The company blames the construction problems on the “variable nature of the soils involved” and the “contractors’ failure to use appropriate means and methods of grouting these soils,” according to court documents.

It also claims that city officials were involved in making many of the decisions that led to cost overruns.

After it became clear that the grouting method wouldn’t work, city officials opted for the “least risky and most costly cure” in order to minimize the political costs, according to BergerABAM’s response.

Yakima has changed how its engineering division oversees projects, which used to be run by committee, with employees responsible for a particular step in a project but with no overall manager. Now, each project has one manager.

The change requires more training, but improves accountability and cuts costs, said Debbie Cook, the city’s director of utilities and engineering.

The city began the change several months ago and is about one-third of the way to having a completely trained staff, she said.

O’Rourke said the new approach would have better served management of the Lincoln project.

“Someone should have been on top of those guys a lot quicker. No question about that,” he said.