The upper level is accessed by a private lift, and features a bar, wine fridge and icemaker.
QV records shows the penthouse was last sold in November 2013 for $4.7 million.
Mr Clark told the Herald: "Different entities own different things. Heather's handling all that," deferring to her on the penthouse sale but saying she was unavailable to talk about it.
Barfoot agent Verne Hines said the couple owned six tower floors.
The penthouse had a $4.7 million CV "but if this was overseas, anything like this starts at about $15 million," he said, referring to Sydney, Melbourne and Hawaii.
Annual penthouse body corporate fees were around $29,000.
The block in 97 Jervois Rd, built around 1987, needed more than $6 million of repairs in 2011 and 2012.
Last year, the Court of Appeal upheld a High Court decision stopping Mr Pugh's neighbours from forcing his family trusts to pay a bigger share of the $6 million-plus leaky building repair bill.
It also ruled he must be compensated for being unable to inhabit his huge two-level penthouse on levels 15 and 16 for nearly two years while the place was fixed.
The court ruling also named prominent film director Lee Tamahori, owner of an apartment in the block, as a party to the action.
Yesterday, Mr Hines said Mr Pugh was not the penthouse vendor.
Mr Pugh said issues over the penthouse remained outstanding from his point of view.
"Still waiting for resolution," he said.
Contractor Haydn and Rollett, which carried out repair work on the tower, said the building had had waterproofing issues on the southwest face and the separate fire-stair tower which it had fixed.
SHANGRI LA PENTHOUSE
• 2 floors.
• 384sq m, 3 bed, 2 bath.
• Owned by Mike Clark and Heather Anderson.
• Bought November 2013 for $4.7m.
• $4.7m CV.
• In 17-level Herne Bay apartment block.
Source: QV.