A damaged trail was ''not nice'' for cyclists to ride on, he said.
Doc would take action against any farmer damaging the trail.
In previous similar incidents, both parties had found a resolution, such as formalising an easement with conditions for responsible use.
In the latest Taieri Pet newsletter, trust chairwoman Kate Wilson, who is a Dunedin City councillor and Middlemarch farmer, said there had been some ''disappointing reports of landowners misusing the trail''.
Some farmers were using the trail as a laneway and the hooves of cattle had caused ''significant deterioration'' of the trail surface and it ''detrimentally affects the trail experience'', she said in the newsletter.
Mr Williams, of Middlemarch, said Cr Wilson should have approached farmers directly rather than airing her concerns in a public newsletter.
Some farmers had land on both sides of the trail and needed to cross it, he said.
Cyclists should tolerate droppings being on the trail.
A bit of sheep or cow droppings on their wheels ''wouldn't hurt, would it?
''It'll let them know they're in a rural part of the trail.''
Strath Taieri Community Board member and sheep and beef farmer Mark O'Neill, of Hyde, said after hearing of Cr Wilson's concerns he talked to farm owners near the trail.
A farmer he talked to had six places on his property which crossed the trail.
He had checked three of the crossings and found ''a wee bit of mud'' on the trail, Mr O'Neill said.
''Once the mud dries up it'll be gone.''
Anything left on the trail by farmers could be easily avoided by cyclists, he said.
He had seen no evidence of farmers using the trail as a laneway, Mr O'Neill said.
Cr Wilson, speaking to The Star on Tuesday, said she wrote the ''friendly reminder'' in the newsletter, rather than approach landowners directly because ''it's not my job to be policeman''.
''I don't want anyone getting into trouble but sometimes they need to be reminded they shouldn't be doing things they shouldn't be doing.''
Her main concern was stock damaging the trail surface but if mud or droppings were left on the trail, farmers should remove it.
''It would be nice for farmers at the end of the season to think about cleaning that up.''
SHAWN.MCAVINUE@thestar.co.nz
The Star