St Giles Hospice in Staffordshire and the Great North Air Ambulance are two charities that complain they are missing out as large stores ban local charity boxes in favour of nominated national charity partners.
Peter Holliday, chief executive at St Giles Hospice, said: "Many major retailers have a long tradition of supporting local charities through on-the-counter collection boxes.
"But we, like many other smaller charities, are now being turned away."
Holliday added: "Collection boxes raise the charity's profile in the community. Breaking this bond with retailers means severing important community contact."
Lynn Lavery, collection box fundraising manager at the Great North Air Ambulance, said she had realised that there was "no point" in approaching large stores to ask them to have collection boxes. "It is now very rare to get them in a major outlet," she added.
One problem is large retailers buying up local shops that had previously welcomed collection boxes.
Tesco is one such example: the supermarket giant has one designated charity each year. Last year, its partnership with Help the Hospices, which was supported by Valerie Singleton and Richard Wilson (see picture, left) raised £3m.
Tesco spokesman Tom Siveyer said: "Help the Hospices benefited from the considerable exposure and raised profile of being our charity of the year." He added that Tesco invites charities to book days in its stores to raise funds, which has proved to be a very effective way for local charities to raise money.
Laura Pennycuick, fund-raising co-ordinator at St Giles Hospice, said that while Tesco's support for Help the Hospices was wonderful, St Giles had missed out.