The trust's Otago and Southland area manager, Owen Graham, said he had received calls from the public concerned classic street fronts and buildings were changing, "and buildings don't just grow again".
The council's attitude amounted to "demolition though neglect", he said.
However, Dunedin City councillor and planning and environment committee chairman Michael Guest said the claims were "aggressive" and "plain nonsense".
The council was, in fact, trying to further protect heritage buildings by changing the district plan so heritage precincts, rather than just single buildings, could be protected, he said.
The trust's latest allegations follow criticism by councillors after Carisbrook Stadium and the Athenaeum and Mechanics Institute building in the Octagon were registered as category one historic places.
On that occasion, the trust's proposals were described by councillors as "stupid", "balmy" and "ludicrous".
Mr Graham said developments, such as a proposed apartment and retail development which would demolish four buildings from 372-392 Princes St and replace them with a five-storey building, were destroying Dunedin's heritage character.
He also pointed to a hotel development on the corner of High and Manse Sts, and a proposed development next to the Southern Cross, also on High St, in the old Smiths City building.
In other cases, prominent Dunedin buildings had been left to deteriorate until they were beyond saving, which was "essentially demolition through neglect", he said.
"That, and the effects of gradual loss of heritage, is worrying people. It is an important issue for a community like Dunedin where we pride ourselves on our heritage, and slowly it is disappearing."
The council could offer developers incentives, such as rates relief or a chance to extend the building height.
Earthquake regulations governing heritage buildings were less strict, he said.
Cr Guest said he agreed the council could offer incentives but rejected the notion the council had a wrecking ball policy.
Changes to the townscape section of the district plan would add to heritage provisions and mean the council could protect a wider range of areas.
He said the question was not what the council could demolish, but what it could do better to protect heritage.
The council had learned from mistakes such as the loss of heritage buildings at Cargills Corner, South Dunedin.
However, if the council started imposing prohibitions on developers they might as well just buy all the heritage buildings, something which would cost hundreds of millions of dollars, as developers would be put off investing, he said.
Council resource consents manager Alan Worthington said developers were required to go through a consents process which was publicly notified, as demolishing a heritage building was a non-complying activity.
It was not an easy process so demolishing historic buildings was rare.
Mr Graham said developers needed to realise there were other options which would better fit a streetscape, and the trust could provide information and guidelines.
There had been "fine recent examples" of the re-use and redevelopment of heritage buildings in Dunedin, such as the makeover of two buildings initially earmarked for demolition, one in St Andrew St into a cafe/bar venue, and the redevelopment of the Bracken Court building in Moray Pl after it was extensively damaged by fire in 2005.
