Baru has claimed in his book "Accidental Prime Minister: The Making and Unmaking of Manmohan Singh" that a senior official in the PMO would seek "instructions" from Gandhi on important decisions.
The PMO statement said: "The question about comments of the former media adviser was raised by senior editors when they met the prime minister in October last year. His answer was - 'Do not believe all he is saying'."
In the book that has sent ripples across the political establishment for its timing and content, Baru has said that Gandhi slowly chipped away at the authority of the Prime Minister's Office, created a parallel power structure and left a weakened prime minister who "allowed himself to become an object of such ridicule in his second term in office".
Baru had resigned from the PMO in 2008.
