The head of Germany's migration office also admitted yesterday that up to 400,000 people were in the country under unknown identities.
The figures emerged just two months after unconfirmed reports that the German authorities were urgently searching for 12 asylum seekers who had vanished.
They were believed to have crossed the border using forged passports from the same source as those used by some of the terrorists who murdered 130 people in the attacks on Paris last November.
The latest admission came in a written answer to a parliamentary question from the opposition Left Party. Chancellor Angela Merkel's government said it believed many of those who had disappeared had simply moved on to other countries, while others had 'gone underground illegally'.
Yesterday the interior ministry in Berlin said the figures were inflated by double entries in a database designed to help find accommodation for asylum seekers.
Mrs Merkel has moved to tighten asylum rules in recent months, and economic migrants with no genuine claim may choose to go underground to avoid deportation. On Thursday, the German parliament approved tougher asylum rules aimed at curbing the record influx.
These include plans for an identity document to be issued upon the arrival of a migrant, which would allow authorities to store personal details under a common database to help avoid repeated registrations. The new rules, which include restricting family reunions for some migrants, also lower the hurdles for the expulsion of convicted criminals.
This key measure comes after the new year's rampage in Cologne, where hundreds of women reported being sexually assaulted and robbed in a crowd of mostly migrant men. There is also a two-year ban on allowing asylum seekers to bring their families to the country.
Germany is expecting 2.5million migrants to arrive in the next five years on top of the 1.1million that arrived after Mrs Merkel threw open the doors to refugees.
However, the numbers arriving at its borders have slumped dramatically in recent days with as few as 150 turning up on the frontier with Austria. Slovenia and Croatia said yesterday they planned to restrict the daily number of asylum seekers entering their countries to 580.
Croatian police spokesman Jelena Bikic said: 'Slovenia informed us on Thursday evening that they can receive 580 migrants daily and we have informed our colleagues in Serbia about it. We will stick to that figure also.' Countries have begun tightening their controls after Austria introduced a daily cap of 80 asylum seekers last week.
The measures have left thousands of people stranded in Greece, which is the main entry point into Europe for refugees.
- Daily Mail