Nipon submitted his resignation with immediate effect, addressed to General Prayut Chan-o-cha, the suspended prime minister.
He was appointed to the post on July 10, 2019.
Nipon went to the Central Criminal Court for Corruption and Misconduct Cases later in the day to enter his plea of innocence after the National Anti-Corruption Commission (NACC) got public prosecutors to charge him with dereliction of duty related to a bidding project when he was Songkhla PAO head eight years ago.
The NACC found grounds to charge him with nonfeasance after Nipon refused to approve the payment for two road maintenance trucks to the bid winner, Ponlavit Tech Plus Co Ltd, totalling 52 million baht.
Nipon came to the court with Wasant Sroypisut, former Constitutional Court president who is his defence lawyer, and Suthas Ngernmuen, former justice minister.
“I didn’t want to use my political position to pressure the work of the judges,” Nipon explained on the reasons for his resignation.
He said no one had pressured him to resign and his leaving the job had nothing to do with the next election, which would be held after the current House completes its four-year tenure in March.
Nipon, a Democrat Party deputy leader, said he did not want to wait until the court had ordered his suspension from duty and he thought he had made the right decision to resign.
Nipon said it would be up to the Democrat executive board to decide who should succeed him as deputy interior minister.
Also on Monday, Nipon posted a long message on his Facebook wall to defend his decision not to pay the money to the bid winner eight years ago.
In the post, Nipon alleged that Ponlavit Tech Plus and a rival bidder had fixed prices and submitted falsified documents.
Nipon said had he paid the money, the Sonkhla PAO would have been damaged.
He noted that the Criminal Court for Corruption and Misconduct Cases Area 9 has issued arrest warrants against suspects over alleged collusion in price fixing, and most of the suspects had fled the country. The suspects who have been arrested have been charged in court, Nipon added.
Itthipon Duanduan, the owner of the company, reportedly fled to Qatar on June 14.
Ater Nipon refused to approved the payment, the company filed a lawsuit with Songkhla Administrative Court and has been fighting the case until the Supreme Administrative Court ruled on May 8 this year that the Songkhla PAO must pay 80 million baht to the company, plus interest accumulated during the eight years.
The Supreme Administrative Court reasoned that Ponlavit Tech Plus had won the bid and the allegation of price fixing could not be cited as a reason to delay the payment.
The NACC had earlier explained that the case of price-fixing was separate from the case of dereliction of duty against Nipon as he was required by the law to approve the payment.
In his Facebook post, Nipon maintained he had made the right decision to hold back payments and if he were given a second chance, he would still affirm his decision not to pay the amount to the bid winner.