The environmental charities have asked Mike Woods, a golf course architect, to examine how the proposed resort with championship course could be built without affecting the sand dunes which are sites designated of special scientific interest (SSSI).
However Trump said the revised layout by Woods would not constitute a proper links or championship course.
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This comes after the Trump organisation said amendments were being made to their original plan.
Jonny Hughes, Scottish Wildlife Trust's head of policy, acknowledged the amendments Trumps team were making but said the design by Mike woods shows it is "easily possible" to build the whole course away from the SSSI.
Anne McCall, head of planning at RSPB Scotland, said: "Rather than the minor tweak that their new indicative plans would mean, we hope that they will now agree with us that it's entirely possible for them to have a top golf course without building on the SSSI in the north or the sensitive dunes to the south.
"If the development goes ahead it will come at an environmental price but we can make that price smaller."
George Sorial, Donald Trump's Spokesman, said environmental measures would be taken to preserve the protected area for future generations and that next month's public local inquiry would be the best forum for the issue to be fully debated.
(GK/JM)
