Louise Richards, director of policy and campaigns at the institute, told Third Sector that sources close to the ministry had indicated it was likely to do away with the list, which charities use to find contact details of potential donors and check the accuracy of donor details they have been given.
Organisations that had held meetings with officials at the ministry had told her the department was planning to abolish the list, she said.
The department ran a consultation on changing the edited electoral register from November 2009 until February this year. The edited register, which omits details of people who have asked to be removed from it, is on sale to anyone for any purpose.
It identified a number of options, including abolishing the register as soon as practicable, abolishing it but extending access to the full register and keeping it but imposing restrictions on its use.
The institute responded to the consultation with a letter that said: "The register is the only big source of accurate data of the UK population and their home addresses.
"If charities do not have access to the edited electoral register, this potentially will cost them in terms of lost income through not being able to correctly target mailings and appeals.
"If charities are unable to verify the address accurately, there is more chance of mail being addressed wrongly, which can reduce potential donors' inclination to donate."
Richards said the Ministry of Justice had confirmed its receipt of the letter but had not responded any further.
"I'm worried that this change could get in through the back door," she said. "As soon as we know the shape of the next government, we will be lobbying against the move."
A spokesman for the ministry said all the views put forward during the consultation would be taken into account before the next steps were considered.