The onus is falling on farmers to empty livestock before having it transported, following a recent meeting in Invercargill.
Environment Southland met the Road Transport Association after the regional council fined Titiroa Transport $750 for effluent spillages in Invercargill in February, believed to be the first time such action had been taken.
While the issue remained unresolved, it appears both organisations would support a law change making farmers responsible for effluent produced by their animals which is spilled by trucks.
Environment Southland councillors believe truck companies should refuse to cart stock that has not been left to stand for 12 hours.
The council has also been frustrated by Fonterra's refusal to allow its suppliers to let stock trucks dispose of effluent in their on-farm systems, fearing the transfer of disease between properties.
Road Transport New Zealand forum chief executive Tony Friedlander told councillors truck companies were caught in the middle, with there being no way of drivers knowing how long stock had been left to stand before being transported.
Mr Swinney said in an interview a code of practice had been developed in 1999 between the various parties with an interest in stock movement, and this had established it was the farmers' responsibility to empty stock before it is moved.
He was frustrated at Fonterra's reluctance to allow trucks to use on-farm effluent systems but said an interim agreement has been reached with two transport operators in Southland to use their dumps until after winter.
With the growth in dairying in Southland, Mr Swinney said the issue of stock effluent would grow and while Southland did not have permanent public effluent dumps, it was hoped four would be built soon.
Mr Swinney said Environment Southland had been talking to police about their powers to issue infringement notices for trucks dropping effluent but a loophole in the law prevented police from issuing notices to trucks carrying livestock, something he hoped lobbying by Local Government New Zealand, police, regional councils and the Road Transport Association could change.
Otago Regional Council resource manager Selva Selvarajah said while the council's network of seven dump sites had successfully reduced effluent on roads, it did not excuse farmers from emptying stock before being trucked or truck operators from having storage systems on their trucks and trailers.