A report in The Sunday Times claimed the charity, which has raised £30m to support injured servicemen and women since it was founded two years ago, was "urging people to turn their backs on Britain's leading fundraising website because it takes a 5 per cent cut of every donation pledged".
But Bryn Parry, chief executive of Help for Heroes, told Third Sector the charity did not have a preferred fundraising website. "We have always allowed our supporters to give through the website of their choice and will continue to do so," he said.
"We understand that JustGiving has to make a profit and think 5 per cent is a reasonable amount of money for it to charge," he said.
He said the charity planned to add a section to its website explaining to supporters the differences between the two fundraising websites and how they worked so they could choose which one to use.
Chris Gourlay, the Sunday Times reporter who wrote the story, said he stood by his report.