It hit out after Planning Service Minister Arlene Foster indicated she was minded to accept the private planning application.
Enterprise, Trade and Investment Minister Nigel Dodds responded by bringing to an end preparations to build a complex on site to replace one destroyed by fire in 2000.
The National Trust said it had "grave concerns" over the minister's suggestion that a Giant's Causeway centre should be built by a private developer.
And Moyle District Council is to hold a special meeting of members to debate the implications.
Both parties said they were examining their options.
Hilary McGrady, National Trust director in Northern Ireland, questioned the pursuing of separate private planning applications for a green field development.
She said the Giant's Causeway, owned by the trust, was the Province's most-visited tourist attraction and one of the tourist board's signature projects.
Ms McGrady said the charity would be "astounded if planning permission could be granted to the private developer".
"Any development so close to the Giant's Causeway's World Heritage Site – and particularly on previously undeveloped land – would fly in the face of planning policies for the area," she said.
"Such a decision by the minister could immediately put the World Heritage Site status of the Giant's Causeway at risk."
Ms McGrady said the National Trust remains committed to working with all stakeholders, including Moyle District Council and DETI, to achieve world class, sustainable and economically-viable visitor facilities on the existing site "without violating the principle that there should be no further green field development in the area".
She said: "A huge amount of money and time has already been invested in working towards an agreed solution to the development of new visitor facilities.
"If Mr Dodds is saying that the existing stakeholder process is dead, we are very disappointed.
"We do not believe that the private application currently being considered is the appropriate solution."
Ms McGrady said the trust would "be seeking advice on all our options".
"The over-riding concern for the National Trust is the protection of the World Heritage Site and its setting, and to achieve the right solution for visitors to the site," she added. "In this context we remain committed to working with all stakeholders to achieve the right solution."
Moyle District Council expressed similar surprise to the ministerial decisions "especially given that there has been an ongoing process of engagement with DETI and other key stakeholders over the last number of years". A special council meeting has been arranged for later in the week to discuss the developments.