The Twentieth Century Society (C20) claimed the Deputy Prime Minister's move would leave the council with a large bill if residents decide to contest the proposals.
Prescott's decision means the council's approval of John McAslan's plans to overhaul Erno Goldfinger's Grade II*-listed landmark ( pictured) will stand.
C20 said similar proposals for Southwark's Brandon Estate in the 1950s led to residents taking the council to a Leasehold Valuation Tribunal (LVT).
In that case, the LVT ruled in the residents' favour, costing the council thousands of pounds.
C20 caseworker Cordula Zeidler explained: 'Residents have taken the case further and have now applied for compensation as the window replacement devalues their flats.'
Zeidler added that this situation could also apply to Trellick Tower.
In a letter to the council Zeidler continues: 'We would ask you to put on hold the window replacement planned for Trellick which we feel is in your own interest.
'We are convinced that the planned replacement seriously compromises the architectural merit and financial value of the flats at Trellick and must be rethought.'