The commission decided last week that charities that fail to update their details or submit annual returns will be removed from the register after 34 months.
The regulator is introducing the measures to deal with 17,000 "hard core" charities that are more than a year late in submitting documents.
"The next priority is to find a durable solution to the hard core of smaller charities that have been overdue with returns or updates for a year or more and may have ceased to operate," according to papers produced for the commission's board.
Commission chief executive Andrew Hind told Third Sector that a record proportion of charities were completing returns on time.
"However, some 17,000 charities have remained overdue with their updates for a year or more," he said. "These proposals offer an effective way for us to address this issue and reassure the public that the information on our online register is accurate and up to date."
The new measures will be used from November if a charity has not filed returns to the regulator for more than a year and 10 months. If it does not respond to repeated attempts to contact it over the next year, it will be taken off the register.
Organisations falling foul of the measures will be shifted to a new register of charities, separate from the main list.
The measures will enable the commission to manage the register better, since it does not have the resources to pursue every organisation on the register that may have become defunct.
"To date the measures taken to establish contact with these charities and update the register have proved to be both costly in staff time and ill-matched to the scale of the task," the board papers said.
"There is insufficient resource to enforce compliance at the bottom end of the income scale and to pursue all residual charitable assets."