The Charities Aid Foundation estimates the sector is currently missing out on between £600m and £700m in unclaimed tax relief.
Devised in conjunction with Gain, a Gift Aid recovery consultancy, the HMRC survey asks questions about the ease and usefulness of the current claims system.
Andy Jones, outreach manager at the Inland Revenue Charities office, said the survey was part of an overall drive to speed up and improve the Gift Aid payment process.
Jones said that many of the system's flaws were caused by the R68 form charities have to fill in, which hasn't been updated for a number of years.
Charities often complete the forms incorrectly, he said, which in turn slows down processing.
The department will use responses to the survey and suggestions from its own staff members to improve the running of the scheme.
Jones wouldn't reveal how long some charities have had to wait to receive their payments, but said: "We want 95 per cent of all payments sent to charities within 15 days. That is a vast improvement on the current rate - only 85 per cent are dealt with in that time." In quieter periods, he added, payments might be made in three or four days.
Cathy Pharoah, director of research at the Charities Aid Foundation, said that HMRC was committed to getting charities to make more use of Gift Aid and welcomed "anything that makes the process easier for charities".
She predicted that the £625m currently being collected through Gift Aid could be doubled.
Barry Gower, managing director of Gain, insisted that there were many ways in which charities could collect Gift Aid, even in the most unpromising of circumstances, such as in charity shops or at dinner events.
He said: "There are loopholes that can be exploited, but this should be done very carefully."
The Institute of Fundraising is working closely with the HMRC to promote Gift Aid and other forms of tax-effective giving across the sector.