Roots and Shoots, which offers young people with learning disabilities in south London qualifications in horticulture, relies on the LSC as one of its main funders. It says it was told at short notice earlier this year to submit its funding bid electronically. Linda Phillips, manager of the charity, described the online process as "inaccessible".
Roots and Shoots submitted its online bid within the March deadline, but was told last month that it was incomplete and it would have to wait until September to reapply. This meant the charity would not receive any money until April 2008.
Phillips said the LSC was now helping to sort the matter out. The LSC confirmed it was inviting organisations that had problems to reapply.