The state Department of Health has cited Hawaii’s only remaining sugar plantation for more than 400 alleged violations of clean air rules and assessed a $1.3 million penalty against the Maui-based firm, Hawaiian Commercial & Sugar Co.

DOH officials announced the violations Tuesday based on a review of HC&S reports submitted to the agency.

The violations occurred over five years from 2009 to 2013 at the HC&S sugar mill in Puunene. Most of the violations have to do with excess emissions from the mill and operation of equipment for controlling emissions.

HC&S, which is a subsidiary of Honolulu-based Alexander & Baldwin Inc., has 20 days to request a hearing to contest the alleged violations.

HC&S issued a statement that acknowledged challenges with operating the sugar mill and deviations from required operating procedures for air pollution control. However, the company disagreed with the number of alleged violations and said it intends to contest what it called an "excessive" administrative penalty.

The company also said there is no indication that the deviations resulted in any violation of health-based air quality standards.

"These violations were unintentional, and the result of operating a very complex milling operation, and we regret that they occurred," Rick Volner, HC&S general manager, said in a statement. "Operation of sugar mill boilers is extremely challenging, particularly when combusting sugarcane fiber (bagasse), which has varying degrees of moisture content."

"For over a century, HC&S has placed the highest priority on complying with all environmental regulations applicable to its operations," Volner continued. "We have performed a comprehensive review of our air permit compliance program and have implemented corrective actions to address the matters raised in the (violation notice). We intend to work closely with the DOH to ensure that any deviations from regulatory standards at the Puunene Mill are promptly resolved."