Chief executive Keith Cooper said the decision to sell the three-storeyed 0.33ha George St site, known as Harvest Court, followed an approach by a buyer with an offer "too good to refuse", and had nothing to do with recent closures of processing plants, he said.
The 3800sq m building was owned by a holding company, Farm Enterprises Otago, which was 74% owned by Silver Fern Farms (SFF) and the balance by Federated Farmers Otago.
SFF would remain the anchor tennant, Mr Cooper said.
He would not reveal the sale price, but according to Dunedin City Council rating information, Harvest Court had a land value of $6.58 million and a capital value of $9 million.
There were eight retail and office lessees on the main-street property.
He said the buyer appeared interested in the potential to develop a car park at the rear of the building as well as its position in the city's commercial centre.
"The money is better in our bank than tied up in property," he said.
While the sale was an unplanned opportunity, Mr Cooper said it fitted with the company's plan to quit non-core assets, which had included the recent sale of a United Kingdom lamb-cutting plant and the closure and sale of a South Otago lamb pelt processing business.
Harvest Court was originally owned by the farming co-operatives Ravensdown, Farmers Mutual Insurance, PPCS (now SFF) and Federated Farmers Otago, but most recently ownership had fallen to the two remaining companies.
In addition, SFF has put its recently-closed Burnside deer processing plant up for tender.
The ageing plant was closed in May with the loss of 138 jobs.
The site consists of 15ha zoned industrial land and 43ha zoned rural.
According to DCC rating information, the industrial-zone land has a capital value of $4.1 million and a land value of $3.6 million.
Mr Cooper said there had been "significant" interest in the Burnside site.