Regular maintenance is needed to avoid breakdowns. Extra space is needed to accommodate the system. Some of the mechanical units are compact and require very little extra space. Two separate manure handling systems are needed -one for liquid and one for solids. While a farmer may have spreading equipment for the liquids, he may have to hire someone to spread the solids or purchase his own spreading equipment.
Some systems have high energy costs to operate.
The different systems have widely varying energy needs. Some may require no energy inputs while others may require several kilowatts of power. There is an increased management requirement. An extra step has been added to the manure handling system. Someone has to take time to make sure the system is operating properly.