The contractor that manages the federal government's underground nuclear waste repository is being awarded nearly $12 million in fees and performance pay for work done while the troubled facility moves toward resuming operations following a radiation leak more than two years ago.

Documents released Thursday by the U.S. Energy Department show Nuclear Waste Partnership — which runs the Waste Isolation Pilot Plant in southern New Mexico — earned about 85 percent of the total awards that were up for grabs for the last fiscal year.

The contractor also received positive marks for work related to recovery efforts, but it was docked for persistent safety challenges, missed deadlines and delays related to the installation of an interim ventilation system that will be key to the plant's reopening.

Citing the calls for improvement outlined by federal officials, watchdogs argued that Nuclear Waste Partnership should have lost out on more of the incentives.

Don Hancock with the Southwest Research and Information Center called the awards outrageous and suggested the system was rigged given that milestones and requirements outlined in the facility's original performance plan were changed midway through the year.

Nuclear Waste Partnership did not immediately respond to a request for comment.

The Waste Isolation Pilot Plant has been shuttered since February 2014, when a container of waste burst and released radiation in the underground facility. Nearly two dozen workers were exposed and monitors at the surface recorded low levels of radiological contamination.

Investigators determined the container had been packed at Los Alamos National Laboratory with incompatible materials, and experts have said the incident could have been avoided.

As a result of the repository's closure, shipments of Cold War-era waste from sites across the country were put on hold and the Energy Department's multibillion-dollar cleanup campaign was sidelined.

Contractors for both the lab and the repository lost out on tens of millions of dollars in fees and performance pay the year before as a result of the incident and the contract to manage Los Alamos will be opened for bid. DOE also agreed to a $74 million settlement with the state of New Mexico.

Top Energy Department officials are pushing to reopen the repository by the end of the year.

In the scorecard released Thursday, a fee official noted what he described as "significant progress" related to the repository's recovery. The document also mentioned improved maintenance for some equipment, the stabilization of areas within the salt caverns where waste is handled and the contractor's ongoing work with the community.