Otago area manager for the trust, Owen Graham, said in a statement yesterday the trust had asked the hotel group to comment on the alleged breaches.
Earlier this year, the group demolished two buildings next to its Southern Cross Hotel to make way for a car park.
Mr Graham said the Historic Places Act required that an archaeological authority be issued before the modification or demolition of any pre-1900 site and any conditions set were required to be met.
"In joint discussions between [the trust] and the Scenic Hotel Group prior to work commencing, we agreed that a bluestone wall and several layers of brick above it would be retained as part of the parking area, and we issued the authority with that as a condition."
In a letter sent on Tuesday to members of Parliament and the media, the group's executive chairman Earl Hagaman said "under duress" from the trust, the company began demolition "with instructions to the demolition company not to remove the blue stone foundation".
"It happened that in destroying the brick wall on top of the bluestone some of the bluestone was damaged."
Mr Graham described the wall as "historically significant".
"The company has now admitted demolishing the wall down to the bluestone, and damaging some of the historic bluestone wall as well, breaching the agreed authority conditions."
Mr Graham said at a meeting last week, the group had accepted the wall could still be retained "in situ".
"They undertook to do what they can to provide ongoing protection and stabilisation for the wall and to get independent advice on how to preserve it."
In his letter, Mr Hagaman questioned the Government's $10 million funding of the trust and he described the trust as being part of a "stifling bureaucracy" affecting New Zealand's growth.
A trust spokeswoman said yesterday increases in Crown funding had followed an independent review that identified certain areas of need.
"This funding is vital for the trust's work in caring for 48 historic properties around the country, which include some notable Otago and Southland places," she said.
