He also faces an allegation of causing serious emotional distress by posting a digital communication, described in court as a poster, on October 4.
The stalking and harassment charge will proceed to a jury trial, while the remaining two charges will be heard by a judge alone.
Zhi is scheduled to return to court for a case review hearing on December 9.
His company, NZAgri Development, has been embroiled in a prolonged dispute with Environment Southland and Southland District Council over thousands of dead lamb and calf carcasses accumulated at its Tuturau property.
Neighbouring residents have complained about offensive odours from the operation, prompting enforcement action and Environment Court proceedings.
Zhi has also been trespassed from the offices of both Environment Southland and Southland District Council following protests over enforcement action against his business.
The stalking and harassment offence, introduced in May, carries a maximum penalty of five years’ imprisonment.
Ben Tomsett is a multimedia journalist based in Dunedin.