Dave Warner with the San Joaquin air district said the agency supports farmers’ efforts to install digesters, but that it has to meet federal standards to eliminate air pollution, or face costly penalties. Meeting those standards has proven difficult in San Joaquin due to natural conditions in the area that trap polluted air. As a result, the district has sought to ensure methane digesters meet strict emissions guidelines - Warner said otherwise, they could become a significant contributor to smog.

“We’ve been working with folks that do want to put in power-production operations at their dairies to make sure they can do so in compliance with air quality regulations,” Warner said.

John Fiscalini, a dairy farmer in the city of Modesto, also in the Central Valley, has run a catalytic converter-equipped methane digester since 2009, after numerous delays caused by regulatory issues. He said the price of the catalytic converters required by the air district’s rules contributed to the system costing more than it brought in, and that operating it forced him to spend a significant amount of time dealing with the district’s concerns. He said on one hand, the state air board had encouraged dairies to invest in digesters to eliminate methane, but then the local aid district had slapped them with added costs for their troubles.

“It bothers me we don't get credit for reducing greenhouse gasses,” he said. “The air board only cares about NOx.”

Interest in digesters among dairies has slumped, partly due to an energy market that is stacked against small producers, but also due to such regulations. Boren said efforts were underway to find more affordable, reliable NOx emissions-reducing equipment. Koetsier also said he’d been contacted by a couple of companies interested in the possibility of taking over operation of his digester to produce renewable energy - a development that may indicate future prospects for the technology. However, as of mid-July he said the system was still idle.

The dairy digester issue isn’t the only example of conflicting policies hampering environmental ambitions and frustrating agricultural businesses. Professor Jay Noel, head of the agribusiness department at the California Polytechnic State University, one of the nation’s leading agricultural schools, has studied California’s regulation of farming. He cited a case in Stanislaus County in the Central Valley where an agricultural composting program run by Stanislaus with the participation of local fruit canneries -part of the county’s efforts to meet state mandated recycling requirements- was threatened by the Central Valley Regional Water Quality Control Board pursuing its own environmental priorities.