For the first time, the FBI and the federal citizenship agency are setting a schedule to eliminate the large backlog of applications that has kept some immigrants waiting for years to become citizens.

The agencies are projecting that 98% of all security background checks for citizenship applicants will take only 30 days by June 2009. They said that “more difficult name checks,” usually for people who have the same name as someone with a criminal record, or who appear on a terrorism watch list, would be completed in 90 days or less by next year.

The FBI name checks have been the major factor in delaying thousands of applications since stricter security requirements were implemented after the terrorist attacks of September 11, 2001. The application backlog also grew significantly longer last summer, when a surge in applications preceded the implementation of higher service fees by Citizenship and Immigration Services, partly to pay for the added staff necessary to speed the FBI name checks.

By May, the agencies said that all name checks that have taken longer than three years would be completed, while all two-year-old name checks are projected to be finished by July.

Yesterday, CIS announced that it was processing applications this year at a much faster clip than in the past, projecting that it would finish more than 1 million naturalization cases in fiscal year 2008, 36% more than the number completed last year.