Synlait shares fell as much as 6 per cent to $9.90 in morning trading but had recently recovered to $10.28.
The company says it has acted "in accordance with legal advice at all times in respect to the land at Pokeno."
That land had been rezoned from rural to industrial, and other industrial developments, including another dairy plant, have been built on nearby land, it says.
The Yashili New Zealand Dairy Company has built a milk processing plant on land across the road from Synlait's land but which isn't subject to the same covenants affecting Synlait's land.
Another dairy company, Winston Nutritional, is planning to build a milk products factory on the other side of the Yashili property on land that is also not subject to such covenants.
Synlait says it had been confident that the land covenants were no longer relevant and that was confirmed by the High Court decision removing the covenants
"It made sense that, as a result of zoning and proper planning that allowed for industrial zoning, that the land covenants would be removed by the court, which they were," Clement says.
Synlait had only taken legal title to the land after the High Court decision, he says. "We intend to continue with our plans at Pokeno."
However, the judgment says that Synlait had started earthworks in March last year and started building the factory in May after gaining resource consents.
The Pokeno plant is due to be commissioned for the upcoming 2019/20 dairy season.