Biometrics Commissioner Alastair MacGregor said police were "risking public safety" by failing to apply for extensions to hold DNA profiles of suspects who have not been convicted.
He also said some records which were still stored should have been removed.
The Home Office said the system worked well "in the vast majority of cases".
A new system limiting DNA record storage was introduced in October 2013.
Previously, DNA profiles and fingerprints could be stored indefinitely, regardless of whether someone had been charged or convicted.
The anomalies were revealed in the commissioner's second annual report since the new rules were introduced.
The report also revealed that DNA profiles and fingerprints of 7,800 people were held on a separate police counter-terrorism database as of October last year.
The database holds biometric records of those convicted in relation to terror investigations and others who have not been convicted but where retention is deemed necessary for national security purposes.
It also allows for the extended retention of material taken from an individual who has not been convicted when a senior officer makes a national security determination (NSD).
Of the 7,800 individuals, 4,350 - or around 55% - had never been convicted of a recordable offence.
Source: Biometrics Commissioner's annual report, 2015, and Home Office and National DNA database annual report
The commissioner's report suggested the new system had led to a series of problems which meant DNA profiles were not being stored when they should be, and that some records had been retained when they should have been deleted.
Mr MacGregor said the DNA profiles of 450 innocent people were automatically deleted from the database before police could decide if they wanted to keep the information on national security grounds.
He blamed "procedural errors and delays" - and said police would have applied to hold about 10% of the records.
"Those errors and delays have led, or will lead, to the loss of a significant number of biometric records that probably could and should have been retained."
A spokeswoman for the National Police Chief's Council said: "The fingerprint and DNA data of a small number of individuals who potentially pose a threat to national security have been deleted from biometric databases as the retention period expired before a national security determination could be submitted for approval.
"The identity of these individuals is known and the risks they potentially pose are being managed in conjunction with partner agencies.
"Comprehensive measures have been put in place to prevent the loss of further biometric data from individuals of concern before a NSD is applied for."
By BBC home affairs correspondent Danny Shaw
The previous system for storing DNA was eventually declared to be unlawful - but it had the advantage of being simple to execute.
The scheme the coalition government replaced it with is proving to be the exact opposite: difficult to understand, unwieldy to operate and prone to error.
Perhaps it's not surprising then that the Home Office has taken three months to publish this report which sets out the many failings.
Solutions are hinted at, such as limiting police discretion over profiles from non-convicted people and having a fixed period of time to keep them.
It won't cure all the problems, but it might help.
The commissioner also criticised police forces in England and Wales who he said had failed to seek extensions to retain DNA profiles of people suspected, but not convicted, of sexual or violent offences.
Such profiles can be held for up to five years, with permission.
He said it could mean crimes went "undetected or un-prevented".
The report said there were continuing difficulties with storing samples from people convicted of serious crimes outside England and Wales, adding "no substantive progress" had been made on the issue.
It said "widespread uncertainty" over police bail powers had contributed to the deletion of biometric records of suspects who have been released after questioning but who remain under investigation.
And it revealed up to 50,000 records of under-18s on the Police National Computer (PNC) may be incorrectly showing that their DNA profiles need to be erased after five years, when they should be stored indefinitely.
However, a number of problems have emerged which indicate that profiles are being wrongly kept on the database, including 4,650 profiles of people classed as "Wanted/Missing" on the PNC.
Mr MacGregor, who is leaving his post after three years, said he also raised concerns with the Home Office about "unlawful matches", in which DNA profiles wrongly retained have been linked to crime scene samples, but has yet to receive a "substantive response".
The Home Office welcomed the report, saying it stated "that in the vast majority of cases the DNA and fingerprint retention system is working properly".
Hundreds of DNA and fingerprint records that could have been held for national security reasons in England and Wales have been deleted, a report reveals.