The 1.7ha industrially zoned site, in Timaru St, was listed for sale at $2.4 million in late-2005 and sold for more than $2 million in November that year to Calder Stewart Industries.
Demolition was completed by late-2006.
Construction has started at the site and Calder Stewart director Alan Stewart confirmed the development arm of Calder Stewart Industries had negotiated a design and build contract with the ministry, which will then lease the building from Calder Stewart, without an option to buy.
Ministry of Fisheries communications manager Barbara Crocker said all 22 Dunedin staff would be relocated to the new site by January, drawing together the storage, laboratory and office personnel from three sites at present leased in Dunedin.
The new single storey building, leased by the ministry for $237,000 a year, will have 618sq m of office and amenities space, a 300sq m warehouse and a 77sq m laboratory It was understood to be a multimillion-dollar development, but Mr Stewart declined to reveal the cost.
He said the ministry would take up about 25%-30% of the site's footprint, "as part of a staged development", but no other parties were involved at present.
Calder Stewart's property division maintains large land-banking holdings around Dunedin, often negotiating with would-be tenants before investing in design and construction, lease-back and sale options with retailers.
During the past 30 years, the Timaru St site has accommodated the Shoreline, Nova Bar and Regines nightclub before being sold by the Shoreline Christian Centre in 2005.
The Shoreline was bought by the Oamaru Licensing Trust in December 1993 for $1.5 million, then sold to the Word of Life Church in 1999, making about $940,000 on the sale.
For five years, the house bar, dining facilities and 36-room accommodation block were leased out by the church.