The U.S. Environmental Protection Agency slapped a state agency with a $100,000 fine yesterday for failing to close large cesspools at an affordable-housing complex on the Big Island.

The fine comes five years after an initial EPA deadline expired for closing large cesspools operated by public and private owners.

Still, more than 100 large cesspools — defined as serving at least 20 people or handling more than 1,000 gallons of waste water daily — remain operating under extended or expired deadlines.

Single-family home cesspools are excluded from the ban.

Cesspools are covered pits in the ground that allow sewage solids to settle on the bottom while dispersing effluent into the surrounding soil.

The EPA ban was announced in 1999 to eliminate potential contamination of ground water and the ocean. While applied nationally, the ban has had its biggest impact in Hawaii, which the EPA said uses cesspools more widely than any other state.

The fine announced yesterday applied to 13 cesspools at the Jack Hall Memorial Housing complex in Kailua-Kona.

The 48-unit housing complex built in 1979 is operated by a nonprofit on land leased from the Hawaii Housing Finance and Development Corp., an agency that helps develop affordable housing.

A predecessor state agency to HHFDC had entered into a consent agreement in 2005 to close the Jack Hall housing cesspools by March 1, 2009.

Earlier this year the EPA expressed frustration about the lack of apparent work to close the cesspools despite a new county sewer line being installed in the area in early 2009, and informed the state it would impose a fine.

HHFDC agreed to the fine and a new deadline to close the Jack Hall housing cesspools by March 2011. The agency estimates it will cost $931,000 to connect the housing project to sewer lines. A private, nonprofit corporation is responsible for the construction cost but doesn’t have enough reserves for the work. Financing options are being explored.

HHFDC’s predecessor was one of five government entities in Hawaii — along with Kauai County, the National Park Service, the Army and the state Department of Land and Natural Resources — that missed the 2005 deadline and entered into consent agreements with and secured deadline extensions from the EPA.

HHFDC and the Hawaii Public Housing Authority, which were created from the 2006 breakup of Hawaii Community Development Corp., were in charge of closing 230 cesspools. Of those, 127 face a June 30 closure deadline. The other 103 faced a March 1, 2009, deadline.

The Public Housing Authority is in charge of most of the 230 cesspools but has not been fined, according to Barbara Arashiro, the agency’s executive assistant.

Other cesspools overseen by the two agencies missed the 2009 deadline but have been making progress toward compliance and have not drawn fines.

HHFDC is one of several Hawaii cesspool owners to be fined by the EPA in recent years.

Other penalties include a $75,000 fine against Costco Wholesale Corp. in 2006, $75,000 against Mauna Loa Macadamia Nut Corp. in 2008 and $110,000 against Gay & Robinson earlier this year.

"EPA will continue to bring compliance actions to protect Hawaii’s water resources," Alexis Strauss, Water Division director of the EPA’s Pacific Southwest region, said in a statement. "While many large-capacity cesspools have been closed, those owners and operators who still have such waste-water systems are overdue in taking steps to comply with the 2005 ban."

David Albright, manager of the EPA Pacific Southwest region’s Ground Water Office, said restaurants, hotels, office complexes and multiunit dwellings in Hawaii still operate outlawed cesspools.