A-EM Architects has been forced to resubmit its design for a small external extension to the Modern masterpiece amid fears that it would affect the building's original fabric.
The building is expected to be upgraded to its new listing status by spring of this year - a move which would make it more difficult to implement external changes.
A statement issued by the council said: 'EH and Lambeth were concerned about the extent to which the proposed new decking obscured the original fabric of the Grade II*-listed building.
'The architect subsequently withdrew the application.'
Jon Wright, case officer for the Twentieth Century Society, was damning of any attempts to change the exterior of the building.
He said: 'It is these types of tiny changes over the years that can take away the monumentality of this building.
'With internal changes, such as the modifications made by Stanton Williams Architects, the building is more malleable, but these series of external changes will detract from a key building. We are disappointed that we were not included in the consultation process.'
EH has been quick to quell any rumours of a falling out with A-EM, but is understood to have been unhappy with the original designs.
A statement by the conservation group said: 'EH and A-EM Architects have reached a good-natured compromise over the small matter of extending the decking outside the new café at the National Theatre.
'Discussions of this detail did in no way negatively affect the working relationship between EH, A-EM and the National Theatre.'
A-EM Architects has since revised its designs, and has resubmitted the proposals for planning. The practice said it hopes to gain planning in April.