Property services director Barry MacKay said one of the reasons there would be a difference was that insurance covered only reinstatement of buildings, and not improvements to them.
"It makes sense for the university to take the opportunity to make improvements where it can during the rebuilding," Mr MacKay said.
The university's Christchurch campus is used by the medical school for teaching and health research and many of its buildings remain closed, due to quake damage.
The main school of medicine building is expected to be fully reopened in the second half of this year.
Mr MacKay said there were no "firm expectations" yet about how big the gap between the insurance cover and the final cost would be.
The picture about final costs and the difference would probably not be known until early next year.
The university was negotiating with its insurers over its final settlement.
"It is difficult to say how long negotiations will end up taking, but there have been no major problems to date," he said.
Up to March this year, the university had spent $870,000 on rebuilding the Christchurch campus, "much" of which would be recovered through insurance, the university's financial review said.
In March, the university also spent $5.5 million on land next to Christchurch Hospital to "consolidate" its operations in the city.
