In April, the Governor proposed a plan to phase out the lagoon system over 10 years while engineers devise safer methods for disposing of the hog waste.
The hog waste flows through slotted boards in the barns to a cellar, and then is carried by plastic pipes to a waste lagoon.
His son is operating an experimental farm that draws off the solid part of the hog waste and sells it to a worm farmer.
The water, which is full of hog waste, is then spread over cropland as fertilizer.
After September 1999, when Hurricane Floyd swirled hog waste into waters throughout the eastern part of the state, pressure to solve the problems grew intense.
The berm wall gave way allowing two million gallons of hog waste to spill into the Kishwaukee River.
The 2005 spending bill includes $1 million for the Missouri Pork Producers Federation, to see if hog waste can be used as a source of energy.
There are also growing concerns that the company's hog waste could pose dangers to local water supplies, and that giant hog operations could cripple small farmers.
Emissions of methane and hydrogen sulfide from hog waste, made without any permits for emitting air pollution, were also a serious concern, Mr. Nixon said.
Recalling his youthful summers at the family farm in Tennessee, he said his father "taught me how to clean out hog waste with a shovel and a hose."