The trial, involving 10,000 volunteers across four sites, was due to begin in February but problems with the system, developed by Atos Origin, meant it was delayed until the end of April.
The delays in the trial were caused by problems with the hardware, software and the capture and recognition of data, according to a briefing paper from the Passport Service.
Remedial action was taken for several weeks but the system was withdrawn for re-configuration.
Yet last week, MPs testing the iris-recognition technology were told that up to 7% of scans could fail, due to anomalies such as watery eyes, long eyelashes or hard contact lenses. MP Bob Russell said the scans could adversely affect people with eye problems.
Mark Blowers, senior research analyst at Butler Group, said the government should look beyond biometrics for authentication.
"The problems highlight the fact that biometrics is in its early days - you have to question whether it is mature enough to roll out to millions of people."
A Home Office spokesman said, "The professional approach is to ensure that any trial be correctly configured and proven before we take it into service."
Speaking at a Home Affairs select committee last week, home secretary David Blunkett said the whole point of the trial was to learn lessons such as this. "It is important to get it right, rather than to get it quickly," he said.
Atos Origin and NEC, which is providing the fingerprint-recognition technology for the project, said they had nothing to add to the Home Office statement.