The institute wants large charities that work on both sides of the border to take part in the event, which it hopes to hold in November.
Kate Higgins, manager of the Fundraising Standards Board in Scotland, said she welcomed the decision as a positive development.
"This is an issue that has the potential to cause serious complaints and difficulties for our members," Higgins said. "If it is something we can head off before that happens, it is a good thing."
The agenda for the meeting has not been set, but the institute is inviting charities that are interested in taking part to put forward topics they would like to discuss.
One potential subject for discussion is the issue of how charities that are based outside Scotland inform the Scottish public about where and how they spend funds they raise north of the border.
Recent research suggests, for instance, that a majority of Scots are unaware of the fact that the RSPCA does not operate in Scotland. Partly in response to that research, the Scottish Society for the Prevention of Cruelty to Animals is running an awareness campaign on inflatable billboards in Scotland that bears the message: "The SSPCA starts where the RSPCA finishes ... at the border!"
Michelle Feenie, marketing manager of the SSPCA, said: "It is vital that we not only continue to raise the SSPCA's profile, but that we also do so in a context that makes it clear that the society is Scotland's national animal welfare charity."
Feenie said that an argument could be made for stopping English and Welsh charities from fundraising in Scotland, but the most important thing was to ensure that any advertising informed the public about where charities operate.
"Failing to do so would only add to the public's confusion," she said.
She added that the SSPCA's inflatable billboards provided the novelty value that its campaign required, and the fact that they were mobile meant the society could move them between locations and so maximise their exposure.
So far, they have appeared in a range of locations across Scotland, including outside the Glasgow Royal Concert Hall and near Edinburgh Castle.
Feenie said: "In order to maximise impact, we haven't had the billboards anywhere for longer than two days."