Hawaii’s two most valuable farm crops — seeds and coffee — suffered production declines in their most recent season, according to the latest annual government estimates.

Coffee had the larger decline as farmers struggled with the recent spread of a potentially devastating virus throughout the island chain, though higher prices generally paid to growers offset some of the financial impact.

The U.S. Department of Agriculture’s National Agricultural Statistics Service estimated that statewide coffee production dropped 15% to 22.7 million pounds in the 2020-21 season from 26.9 million pounds the season before.

However, the value of the most recent season’s coffee crop declined by a little less, or 11%, to $48.4 million from $54.3 million because the average price paid to farmers per pound of coffee rose to $2.13 from $2.02 in the year-over-year period.

The agency’s report said heavy rainfall in some areas hurt production, though bigger issues involved the coffee berry borer, a beetle, and coffee leaf rust.

Infestations of the coffee berry borer were recently detected on Kauai and Lanai after being established on Maui, Oahu and Hawaii island.

The leaf rust, a fungus that wiped out a vast coffee industry in Sri Lanka after it was discovered there in 1869, was detected in Hawaii in October.

About a week ago the U.S. Environmental Protection Agency approved off-label use of a fungicide to combat the fungus on Hawaii coffee farms. The fungicide, Priaxor Xemium, doesn’t have regular EPA approval for use on coffee plants, but is approved for use on other food crops, including strawberries, tomatoes, potatoes, sugar cane, soybeans and wheat.

Under the EPA’s emergency exemption, the fungicide can be used on Hawaii coffee plants for up to one year or until such use is added to the product label by the EPA and the fungicide’s manufacturer, BASF.

The state Department of Agriculture said the leaf rust can produce crop losses of 30% to 80%.

“Coffee leaf rust is a plant pathogen that cannot be eradicated once it takes hold, so it’s important that we use all available tools, including the use of fungicides, to help manage the problem,” Phyllis Shimabukuro-Geiser, the department’s director, said in March.

According to the Hawaii Coffee Association, nearly 1,500 coffee growers statewide are vulnerable to the fungus, which can wipe out entire farms in a matter of weeks because rust-resistant varieties of coffee aren’t grown here.

“We’re facing the most destructive coffee disease in the world,” the association said in February.

In Hawaii’s seed industry, where several giant agribusiness companies mainly breed corn seed varieties that they ship to the mainland for large-scale reproduction that gets sold to farmers, projected shipments declined by 6% to 3.83 million pounds during the 2020-21 season from 4.06 million pounds shipped during the previous season.

The USDA report suggested the decline was due to a 7% reduction in the number of acres planted for seed production, or 2,185 acres in the recent season compared with 2,360 acres in the season before.

Because the seed grown in Hawaii is not sold, the USDA values the industry based on operating costs. The agency’s report estimated that this value slipped 2% in the recent season to $107 million from $109 million the season before.

Hawaii’s seed industry value has generally been on a gradual decline for a decade after peaking at $242 million in the 2011-12 season.