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However, trust chairman Stephen Jeffery said it was a tree branch that did the trespassing.
As part of a formal survey, which the Johnstons commissioned, pegs connected by string were erected to mark the boundary of their land and the marginal strip on which the trail is being built.
Mr Jeffery said when the contractors were clearing some trees from the marginal strip, a branch fell on the string and the tension caused two of the pegs to come out.
He recently received a letter from Checketts McKay Law which said about December 7, two pegs had been knocked over.
"This is a trespass and we have contacted the Alexandra police," the letter said.
Mr Jeffery said he had not been contacted by police.
Central Otago police sub area commander Senior Sergeant Ian Kerrisk said he had no record of any complaint.
He said police were aware of the ongoing dispute between the Johnstons and the trust but this type of event would not be a matter police would get involved in, though it could be taken through civil court.
When contacted by the Otago Daily Times yesterday, Bruce Johnston declined to comment.
Lawyer Russell Checketts could not be reached for comment.
Mr Jeffery said he was "obviously disappointed that it's got to this stage".
Construction of the first 10km of the trail from the Alexandra end started early last month and Mr Jeffery said it was making good progress.
It is expected to be completed by June.
John Sutton Contracting has recently begun blasting to clear the route of large rocks.
The trust is still in the process of negotiating with landowners from the Roxburgh Hydro Dam 10km back towards Alexandra but Mr Jeffery said this was "looking positive".
Construction of this section is expected to begin within a year.
The middle section is still contentious as the Miller family, who farm The Herrons Station, are adamant the trail will not cross their land.
The trust intends to boat cyclists past The Herrons.
The total cost of the trail has been budgeted at $3.4 million.