The settlement resolves a federal civil case against the companies.

The case had been stayed between December 2008 and March 2012 to allow the Department of Justice to complete its criminal probe into the April 2007 collapse, which killed six miners and three rescuers.

The US Mine Safety and Health Administration, which led the federal investigation, found a “grossly deficient mine design” led to pillar failures at Crandall Canyon. It subsequently issued 20 enforcement violations to the operator and assessed $1,639,351 in penalties.

Under the settlement, Murray and its subsidiaries – Genwal Resources and Andalex Resources – accept four of the citations and orders as contributory, meaning that the company’s violations contributed to the cause or effect of the accident.

Those violations, MSHA said, included the improper mine design as well as a repeated failure to revise the mine’s design, despite knowledge that it was inadequate.

Additionally, the companies agree that three of the standards violations will be classified as flagrant. Such infractions carry the highest penalty assessment under federal law.

Two of those flagrant violations are directly linked to criminal charges brought by the US attorney’s office in Salt Lake City in March 2012. Genwal Resources pleaded guilty to both.

A third flagrant violation involves a failure to improve mine design following an August 3, 2007 coal burst – just three days prior to the first fatal accident that took six of the nine lives. The second collapse occurred August 16.

Genwal Resources and Andalex Resources will pay a total $949,351 in civil penalties in the settlement deal, following some modifications to the enforcement actions. Three of the enforcement actions carrying a total $340,000 in penalties were vacated.

Also, the Murray Energy subsidiaries will pay $200,649 to settle other violations committed at mines in Utah, with no modifications made to those citations or orders.

“In this settlement, Genwal Resources and Andalex Resources have acknowledged responsibility for the failures that led to the tragedy at Crandall Canyon,” solicitor M Patricia Smith said.

“These failures resulted in the needless deaths of nine members of the mining community.”

MSHA assistant secretary Joe Main said the settlement’s violations supported its investigation findings.

“This was a tragedy that should never have happened,” he said.

“Miners deserve to return home after a shift in the same condition they left. MSHA will continue to fight for that right on behalf of our nation’s miners.”

The settlement has been filed with Federal Mine Safety and Health Review Commission administrative law judge Richard Manning for his consideration.