New Jersey Transit is cleaning up its fleet.

The nation’s third-largest mass-transit provider has agreed to spend $395 million over the next six years to purchase 772 commuter coaches that use advanced clean-diesel technology.

The deal with Motor Coach Industries, a bus manufacturer in Des Plaines, IL, will let NJ Transit replace older vehicles, many with more than 500,000 miles on the odometer. The agency has bought more than 2,000 buses from the company since 1982.

NJ Transit estimates the new commuter coaches will enable it to boost seating capacity by six percent. The buses each seat 57 passengers. The contract was signed earlier this month, and delivery will begin in 2016.

Clean diesel is a new generation of technology comprising a three-part system that combines cleaner fuel, advanced engines, and more-effective emissions control.

“These buses will play a key role toward improving air quality in the region through gains in ridership and also the environmental performance of these new coaches as they are put in service,’’ said Allen Schaeffer, executive director of the Diesel Technology Forum, a nonprofit organization.

NJ Transit has one of the largest coach fleets in North America. Schaeffer said the acquisition sends a very strong statement about the value and benefits of clean-diesel technology in a competitive green-technology space.

In 1999, NJ Transit purchased 50 coaches that used compressed natural gas from MCI in a pilot program — a first for any U.S. public-transit agency. The next year, it added 27 more such vehicles.

The agency has relied on commuter coaches as the mainstay of its express service, said Rick Heller, president and CEO of MCI. The announcement “for 772 additional vehicles marks another milestone,’’ Heller said.

According to research commissioned by the Diesel Technology Forum, just under 41,000 heavy-duty vehicles in operation in New Jersey come with an engine that meets federal emissions standards, beginning with model year 2010. As a result, nitrogen-oxide emissions, which contribute to smog, have been reduced by 300,000 tons. In addition, 150,000 tons of carbon emissions, which cause global warming, have been avoided.

Smog, or ground-level ozone, is New Jersey’s most persistent air-pollution problem. The state has never met the federal health-quality standard for the pollutant.