Liberty, formerly the National Council for Civil Liberties, says it is not against the plans in principle, but will look closely at the proposals to ensure they do not infringe the basic rights of individuals.
The Department for Education and Skills has started consultation on the feasibility of using a single "learner identifier" as a better way to track students' progress through post-16 education.
It is intended for the number to "replace the plethora of other 'unique' numbers and identifiers and to provide one single learner number that would be used across the learning sectors".
The DfES said that stakeholders indicated a strong preference for the number to be issued to all young people during Year 10 at age 15. For the rest of the population it is likely the number would be issued during their first engagement in learning after the system "goes live".
One suggestion under consideration is that the unique learner number might be held on some type of smart card, similar to the Connexions Card, leading to concerns that it will be a precursor to a national identity card.
Liberty this week expressed concern that the information collected could fall into the wrong hands. A spokesman said: "This Government has a mania for collecting data on people. If it can be shown that the purpose is to be of benefit to the student then fine, but one is sceptical because of the previous record of this Government.
"If information is going to be collated and stored we need to know what safeguards are in place to prevent that information being passed to a third, fourth, or fifth party."
Liberty also questioned how the information would be safeguarded. The spokesman added: "At the moment it is quite difficult to steal somebody's degree or qualifications. But while you have information stored electronically, it is possible for people with certain skills to be able to access it. If it is possible for teenagers to hack into the Pentagon's files, can anything be secure?"
Since 1999 a "unique pupil number" (UPN) has been issued to all children when they start at state schools and which records their progress through national tests at seven, 11, 14, and at GCSE.
There were protests last year when schools were for the first time asked to provide the name, address, and post code of pupils, along with their UPN, their ethnic origin, free school meals entitlement and other personal details when completing the annual census.
One advocacy group, Action on Rights for Children in education (Arch), accused the Government of attempting to create a national identity scheme for children.
The DfES insists the concept of the unique learner number "is set within the context of the commitment to reduce bureaucracy, raise standards, and increase levels of participation and achievement across the education and lifelong learning sectors".
It claims the number is also intended to help track students when the credit-based system of qualifications, now being planned, comes in.
The Association of Colleges has been invited to take part in the consultation, which began on December 1 and runs until March 5.