The Interior Ministry said the missing files concerned people who had been arrested and later released.
However, the Labor Party said the move posed "enormous risks" to public safety.
The removed data was in his database Police National Computer, one systemic which stores and discloses criminal record information throughout the UK.
It is used to assist police investigations and provide real-time checks on people, vehicles and crimes, as well as whether suspects are wanted for other offenses.
Attempted cyber attack on the database, however, has been ruled out.
In a statement, the Interior Ministry said the incident had been resolved and "we work with law enforcement partners to assess its impact".
"The issue concerned people who were arrested and released without further action and no records of criminals or dangerous persons have been deleted. No further files can be deleted. "
the minister Nick Thomas-Symonds called the minister Priti Patel take responsibility for the database error and be clear about the impact it had.
"The Minister of the Interior must take responsibility for this serious problem", he said.
"He urgently needs to make a statement about what has gone wrong, the extent of the issue and what steps he is taking to reassure the public. Answers must be given. "
"This is an extremely serious one security breach which poses enormous risks to public safety. "
The incident comes shortly after the removal of some 40.000 alerts about European criminals from the same database.