ROSEMOUNT — Flint Hills Resources wants to spend $400 million to upgrade its refinery in Rosemount, a plan that would improve the facility’s efficiency but also increase its output of greenhouse gases.

The company filed an application Friday asking the Minnesota Pollution Control Agency to amend the air-quality permit for its Pine Bend Refinery.

The proposed improvements would allow the refinery, about 20 miles south of St. Paul, to come closer to its processing capacity of 320,000 barrels of crude per day and also reduce emissions of nitrogen oxide and sulfur dioxide, spokesman Jake Reint said.

However, the upgrade will increase the output of carbon dioxide, a greenhouse gas linked to climate change. The Pine Bend refinery, the largest in Minnesota, currently contributes about 3.5 million tons of carbon dioxide, or 2 percent of Minnesota’s total greenhouse-gas emissions, according to Flint Hills.

“That isn’t expected to change significantly as a result of these projects,” Reint said.

The upgrade would be the largest at the refinery since 2006, when it completed a $350 million project to produce a diesel fuel containing substantially less sulfur.

Before it can make any changes, the refinery would have to get approval from the Pollution Control Agency to amend its air permit to comply with new greenhouse-gas standards drawn up by the U.S. Environmental Protection Agency.

If approved, the projects would double the size of average daily contract workforce to more than 1,000 workers, Reint said.

He also said the company hopes to start work in 2014 if the Pollution Control Agency approves the air-quality changes by the end of next year.

Flint Hills says its Pine Bend refinery has reduced its on-site emissions in 10 of the past 11 years. The new projects will further cut nitrogen-oxide emissions by 20 tons per year and sulfur dioxide emissions by 10 tons per year, Reint said.

Nitrogen oxide can combine with volatile organic chemicals to create ozone, an element in smog. Sulfur dioxide is the main component of acid rain.

Flint Hills, based in Wichita, Kan., is a wholly owned subsidiary of Koch Industries Inc.