His departure adds to the struggle faced by centre-right Prime Minister Mark Rutte as he tries to counter a surge in anti-immigration populists who look poised to win big in the elections on Thursday.
Harbers was caught out over a report featuring statistics on crimes perpetrated by asylum-seekers in the Netherlands that he presented to parliament.
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In the report, misdemeanours such as shoplifting had their own separate categories but serious crimes such as sexual assault, murder and manslaughter were lumped together under the category 'other' with no disaggregation.
The revelation of that omission by the newspaper De Telegraaf triggered anger among lawmakers, some of whom questioned whether it was a deliberate attempt to skew reception of the report.
Late Tuesday, during a parliamentary debate, Harbers announced he had offered his resignation. He assumed "total responsibility" for not correctly informing the chamber but said it was "not deliberate," Dutch media reported.
Rutte responded by saying he 'respected' Harbers's decision to step down, but declared on Twitter that it "incredibly regrettable that the cabinet must say goodbye to such a talented and committed liberal".
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Rutte's governing coalition already suffered a shock two months ago when provincial elections made the Forum for Democracy party -- an anti-immigration populist party that backs a Netherlands exit from the European Union -- the biggest party in the senate.
The Forum for Democracy is course to possibly beat Rutte's Liberals in the European elections on Thursday.
The Netherlands will be the first EU country -- along with Brexit Britain -- to vote in the polls, which will be held in other European countries over the subsequent three days.
If Forum of Democracy does do well, it would be a bellwether of a populist tsunami that could shake the European Union.
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