One restricted note for Christopher Graham, the Information Commissioner, said: “The case for the retention of this data still needs to be made.
“The value of historic communications data in criminal investigations has not yet been elucidated.”
The ICO is now calling on the Home Office to ensure all relevant safeguards are in place to ensure the programme is not abused.
A spokesman said: “The Information Commissioner's role in this Home Office project, both under this government and the last, has been to press for the necessary limitations and safeguards to mitigate the impact on citizens' privacy.
"Ultimately, the decision as to whether to proceed with the project is one which has to be taken by Parliament."
The Coalition yesterday faced a growing backlash over the move, which is a revival of plans first raised then abandoned by the last Labour government – and which the Conservatives and Liberal Democrats both criticised.
Senior Lib Dem MP Malcolm Bruce warned that the system could be wide open to abuse while Mark Field, a Conservative member of the parliamentary Intelligence and Security Committee, which oversees the work of the intelligence agencies, said he believed that opposition had grown since the last attempt to legislate.
Trefor Davies, Chief Technology Officer at business internet service provider Timico, warned the plans could be "nigh on impossible to enforce" and could drive users underground.
He said: “The reality is that it is nigh on impossible to stop people communicating using the internet without being discovered and attempting to develop a system that will do this is not only likely to be wasted money but will be a step towards entering a category of nation currently occupied by the likes of China and Iran."
Downing Street insisted the power was need to keep ahead of modern technology used by terrorists and criminals and stressed content would not be access.
Nick Clegg, the deputy Prime Minister, whose party normally campaigns against intrusions into privacy, insisted he was “totally opposed to the idea of governments reading people's emails” but that was not the proposal.
“All we are doing is updating the rules which currently apply to mobile telephone calls to allow the police and security services to go after terrorists and serious criminals and updating that to apply to technology like Skype which is increasingly being used by people who want to make those calls and send those emails,” he said.
Security minister James Brokenshire said the emphasis was on solving crime rather than "real-time snooping on everybody's emails".