Sue Brumpton, chief executive of the Public Fundraising Regulatory Association, said the proposed two-tier licensing process could prove "unworkable" in the short term.
If ministers' plans are implemented, charities will initially have to prove they are 'fit to collect' with the local authority where their headquarters are based. They will then have to apply for permission to run collections with each local authority where they plan to be active.
Because many charity headquarters are in London, local authorities in the capital could be swamped by thousands of applications to operate face-to-face and cash collections.
An anomaly in current legislation means that public fundraising in the capital is controlled not by local authorities, as it is elsewhere in the country, but by the Metropolitan Police. This has raised fears about both the capacity and ability of London's councils to cope with their new role.
The implications could be felt by any charity with a London head office, even those that collect in streets outside the capital.
"I can see there being a backlog," said Brumpton. "If charities aren't allowed to collect until it's sorted out, that could be a real worry.
"Years down the line, it could be workable, but when it's first implemented it could be a big strain on those local authorities that have lots of charities to register. There are going to be a lot of applications in Islington."
The association, which represents around 110 charities and 20 fundraising agencies, is using the six-week period of pre-legislative scrutiny, which ends next month, to lobby for a change in the proposed law.
"We will be preparing a briefing for our members to include in their own submissions or asking them to support our submissions," said Brumpton.