The land - which would be retired from grazing - comprised an expansive open landscape containing a wide diversity of tussock grassland, shrub land, wetlands, soaks and rock outcrops.
Bordering the Te Papanui Conservation Park, it had close to 100 indigenous plant species, and more than 90% of the block had been assessed as ecologically significant.
It was also home to several at-risk species, including the New Zealand falcon and the native fish koaro and koura, as well as geckos and skinks. There were also archaeological sites, as gold mining had occurred in the area.
It was Pamu's second-largest covenant after the 1456ha Mt Hamilton covenant, near Te Anau, which was unveiled last year, and added to more than 7000ha the company had covenanted since 1991.
Landcorp was created out of the Department of Lands and Survey in 1987.
Mr Mulligan has had a variety of roles, starting as a field officer of Crown land, based in Palmerston North.
His first association with Waipori was during a three-year stint in Otago, beginning in 1981, as a field officer in land development.
The acknowledgement was a tribute to the Lands and Survey and Pamu staff he had worked with over 40 years, who were passionate about the company's commitment to sound environmental stewardship, he said.
There was also some family significance as his ancestors came ashore on the Otago coastline in 1873, aboard Surat, which was shipwrecked in the Catlins.
''I know the many Mulligans who have worked the land since then would be chuffed to see their name on this significant covenant,'' he said.
QEII National Trust chairman James Guild said the trust had a long-standing relationship with Pamu.
It was good to see the country's largest farmer setting an example of biodiversity protection, alongside production.