A Dutch junior justice minister has quit after his department came under fire for appearing to minimize statistics about criminality among asylum seekers.

Migration minister Mark Harbers resigned on Tuesday in a bad blow to the government just ahead of European elections.

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 quit on Tuesday after he was discredited for his report about criminality among asylum seekers, in which he appeared to have classified very serious incidents such as murder and manslaughter, assault and sexual offenses under the category 'other'

Harbers was caught out over a report featuring statistics on crimes perpetrated by asylum-seekers in the Netherlands that he presented to parliament.

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.

Anti-immigration lawmaker Geert Wilders accused the ministry of 'sweeping under the carpet' allegations of serious crimes among the thousands of asylum seekers in the Netherlands.

Harbers said he assumed 'total responsibility' for not correctly informing the chamber but said it was 'not deliberate'

Wilders said the resignation was 'the only correct conclusion.'

The accusations of a cover-up led to a swift internal investigation at the justice ministry.

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'.

Harbers departure is a major blow to centre-right Prime Minister Mark Rutte ahead of this week's European parliament election

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.