Former Cabinet Office minister Francis Maude told the Conservative Party conference he is worried the GDS will be "scaled back and unwound" under Kevin Cunnington.
He identified that digitising government platforms and making them work across the entire public sector is a necessity and the GDS needs to be protected in order to maintain the UK as a powerful force in digital services.
He told the audience that legacy ways of the government mean it's likely the service will lose its meaning, despite the principles being replicated in the US and Australia.
He fears that the government is trying to de-unify the service and "take it back", which means an end to the innovative thinking and positive impact it set out to achieve.
"You have to drive it centrally, and departments, separate ministries and separate agencies prize their autonomy and they will always want to take it back, and that is now happening," Maude said.
"Just at the moment when the UK has just recently been ranked top in the world for digital government, we are beginning to unwind precisely the arrangements that had led to that and which were being copied in America and Australia and also some other countries as well," he continued.
"This is, for me, a pity - there is a sense these old structures in government, which are essentially about preserving the power of the mandarins, are being reasserted."
However, GDS chief Kevin Cunnington has previously shunned rumours the organisation would be split up, commenting it would remain to be part of the Cabinet Office and its mission remains the same: "to lead digital, technology and data across government."
