Student unions are currently classified as exempt charities, which means they are eligible for the same tax breaks as registered charities but are regulated by their respective universities rather than the commission.
But under the new Charities Act a student union will have to apply to the commission to become a registered charity if its income is more than £100,000.
A number of the UK's leading student unions are keen to register as soon as possible, but a spokeswoman for the Charity Commission said they would have to wait until 2008. She added: "It wouldn't make sense to apply early – a date hasn't yet been set for implementation."
Leeds Student Union recently held a referendum in which 90 per cent of students voted in favour of applying for independent charitable status.
Lesley Dixon, chief executive of Leeds Student Union, said: "It will be a shame if we can't register before 2008. I would have thought the fact that we want to be properly regulated early would be seen as a good thing."
Steve Vaid, chief executive of King's College London Students' Union, said: "We have invested a lot of time and effort to prepare for the transition.
"There's a real impetus for change. We know we can learn a lot from the third sector and think we have a lot to share, too."