"There has been uncertainty over this matter for too long," Ivo Opstelten told journalists at a press conference in The Hague.
"I take full responsibility, so I have just submitted my resignation to the king."
Opstelten and secretary of state Fred Teeven submitted their resignations hours after the ministry said it had found evidence of the exact amount paid to trafficker Cees H at the time - 4.7 million guilders (2.4 million euros).
Last year Opstelten said there was no evidence of the agreement when questioned by MPs following media reports about the affair.
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"The investigation failed to find bank statements or other documents but I have indeed digital proof that the $4.7 million guilders was transferred to Cees H," Opstelten said yesterday.
"I have to find that the information was indeed available and could have been released earlier," he added.