The NL Times cited Harbers telling the parliament that he "felt responsible" for such an interpretation of the figures.
When asked for explanations, he denied deliberately concealing the real numbers, saying that the cases put in the "other" category had not been proven and that some of them were still pending a verdict.
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Harbers is already the third justice minister to have resigned from Prime Minister Mark Rutte's cabinet.
Since 2015, Europe has been struggling to accommodate hundreds of thousands of refugees, primarily from North Africa and the Middle East, as part of its open door policy. The Netherlands, one of the most sought after asylum destinations, has received a total of 5,405 asylum applications as of April 2019.