Police admitted they would not meet a 10 July deadline to disclose files to the court.
Coroner Brian Sherrard said he knew the development would cause "regret and distress" to Arlene Arkinsons family.
He questioned whether the police was diverting sufficient resources to the task.
Fifteen-year-old Arlene, from Castlederg went missing in August 1994 after a night out at a disco in Bundoran.
Her body has never been found.
The inquest had been due to run at the start of September, almost eight years after the first preliminary hearing was held.
However, this was dependent on the PSNI completing disclosure of the case files by 10 July.
A barrister for the PSNI told the preliminary hearing they'd be really pushed to have this done by the end of September.
The coroner said it was with regret that he had to re-list the case for 2 November, and issued the PSNI with a new disclosure date of the end of August.