The committee, chaired by Sir Nigel Wicks, has recommended it be made clear that all ministers, including the Prime Minister, should be responsible for their special advisers, whose role should be spelled out clearly.
The powers of the Prime Minister's two most senior advisers - director of communications and strategy Alastair Campbell and chief of staff Jonathan Powell - came under particular scrutiny.
Their roles should be agreed by Parliament, and their right to instruct career civil servants limited to those in the PM's office, the committee said.
The report has also set out a requirement that appointment panels should be confident of the impartiality of individuals given senior posts within the Government Information and Communication Service.
Wicks said: 'At a time of considerable change within the Government and in the environment in which it operates, we believe it is vital for there to be clarity about boundaries within the executive.'
The IPR welcomed the recommendations. Director-general Colin Farrington said: 'I am pleased that the Wicks Committee has responded positively to IPR's evidence about the need to ensure that special advisers, especially those within Number 10, do not compromise the integrity of Civil Service communication professionals.'