Mr Thomas said there should be full transparency over the plans
A central database holding details of everyone's phone calls and emails could be a "step too far for the British way of life", ministers have been warned.
Plans for such a database are rumoured to be in the Communications Data Bill.
But Information Commissioner Richard Thomas said "lines must be drawn" to defend "fundamental liberties".
The government says the growth of the internet means changes must be made to the way communications are intercepted in order to combat terrorism and crime.
In his annual report, Mr Thomas addressed speculation about plans for a government-run database holding details of telephone and internet communications of the entire British population.
He warned that while "targeted and duly authorised" interception of terrorist and other suspects' communications could be "invaluable" - there should be a full public debate on the justification for such a wide-ranging database.
"Do we really want the police, security services and other organs of the state to have access to more and more aspects of our private lives?" he said in the report.
Later he told BBC Radio 4's World at One: "I'm not saying it's right or wrong but I think there should be absolute full transparency."
He said it may make the work of the police simpler, but added: "We do have to stand up and say these are our fundamental liberties and our freedoms and lines have to be drawn somewhere, and there should be a full democratic debate about where exactly the lines should be drawn."
He told the BBC he was not aware of such a database in any other democracy and said there had not been enough debate on other methods of collecting personal details - like the expanded DNA database.
Speculation that the government is considering collecting the information - including numbers dialled, websites visited and location of mobile phones being used - has increased because it has talked about "modifying procedures for acquiring communications data" in its proposed Communications Data Bill.
Currently police and intelligence agencies can ask telecommunication providers for information on phone calls made, texts sent and internet sites visited.
The provider can query the request, which might then go to the interception commissioner and another watchdog - but under the new proposals, that right would be removed.
In a statement the Home Office, which did not deny plans for a database, said: "The changes to the way we communicate, due particularly to the internet revolution, will increasingly undermine our current capabilities to obtain communications data - essential for counter-terrorism and investigation of crime purpose - and use it to protect the public."
It added that as a result there could be "serious consequences" for police and intelligence gathering.
"To ensure that the agencies can continue to use this valuable tool, the government is planning to bring forward the Communications Data Bill."
It said a draft bill would be published later this year "allowing for full engagement with Parliament and the public".
But the Conservatives and the Liberal Democrats said previous examples of people's personal information being lost, showed the government could not be trusted with it.
Shadow home secretary Dominic Grieve, said the government's record on protecting data was "appalling" adding: "Putting all this data into the hands of the government will threaten our security, not make it better."
Liberal Democrats home affairs spokesman Chris Huhne said the database would be "an Orwellian step too far".
"Ministers have shown time and time again that they cannot be trusted with sensitive data. There is no reason to think they will be any less slapdash with our phone and internet records," he said.
Elsewhere in his report, Mr Thomas notes that he is serving two enforcement notices against HM Revenue and Customs and the Ministry of Defence after "recent high-profile data breaches".
They will have to give progress reports on what they are doing to "improve data protection compliance".
He also points out that 11 people and organisations have been prosecuted by his office in the past 12 months.