The state Department of Transportation has been fined $1.2 million and ordered to correct federal Clean Water Act stormwater violations at Honolulu and Kalaeloa harbors, it was announced Wednesday.

The penalty is part of a negotiated settlement between the U.S. Department of Justice, the U.S. Environmental Protection Agency, the state Department of Health and the state DOT resulting from violations identified during inspections going back to December 2008, said EPA spokesman Dean Higuchi.

In addition, the DOT violated a 2009 EPA administrative order to correct violations and deficiencies in stormwater management plans for the two harbors, according to the settlement’s consent decree.

The settlement requires the DOT to do a better job of preventing contaminated stormwater runoff from reaching the ocean. Stormwater runoff often contains sediments, trash, chemicals and oils that cause environmental damage.

In a statement issued Wednesday, the Department of Transportation said the Harbors Division is already making progress in complying with the settlement.

According to the settlement, the DOT must create a system of project review and inspections, install treatment systems and exercise more control over tenant activities at the two harbors. The requirements include:

>> Creating a new Office of Environmental Compliance to ensure all DOT facilities comply with federal, state and local environmental regulations.

>> Developing a stormwater prevention outreach and training program to communicate with harbor users and inform the public about how their activities affect the quality of stormwater runoff.

>> Ranking all harbor tenants annually based on their activities and risk of pollutant discharges. Inspecting all high-risk tenants twice per year, medium-risk tenants once per year and low-risk tenants every five years.

>> Inspecting stormwater outfalls during wet and dry weather for discharges and assessing the condition of each outfall to determine if maintenance is needed.

>> Establishing a program to control discharges from construction sites. Studying the feasibility of retrofitting construction projects and completing at least three retrofits.

In a statement, the DOT said it has worked to implement programs covering illicit discharge detection, outfall inspections, construction site best management practices, updates to tenant storm water management programs, ongoing training for employees, harbor users and tenants, upgrading inspection protocols and creating an office of environmental compliance.

“The Hawaii DOT has already made major strides in improving storm water run-off management plans in its highways and airports divisions,” interim Director Ford Fuchigami said in a statement. “The creation of the environmental compliance office will ensure that HDOT has staff strictly focused on environmental issues across all divisions — this position will report to the director.”

Jared Blumenfeld, the EPA’s regional administrator for the Pacific Southwest, said in a statement, “By making long-term changes to its operations, HDOT is taking major steps to increase the protection of beaches, coral reefs and water quality on Oahu.”

Gary Gill, state Health Department deputy director for environmental health, added: “With this case settled, we can expect our state government to be a better steward of Hawaii’s clean waters.”

The $1.2 million in penalties will be divided equally between the state and the U.S., Higuchi said.

The consent decree has been lodged with the federal district court by the Justice Department and is subject to a 30-day public-comment period and final court approval.