Meng, who is China's vice minister for public security and a former head of Interpol China, was elected president of Interpol in November 2016.
On Friday, the French Police started an investigation after Meng's wife reported that he was missing.
However, China's anti-graft watchdog said late on Sunday that the Chinese authorities were investigating for suspected violations of the law.
A statement from Interpol confirmed that as per the agency's constitution and internal regulations, the Senior Vice-President of Interpol's Executive Committee, Kim Jong Yang of South Korea, will be instated as the acting president.
The worldwide police agency Interpol announced Sunday that its missing president had resigned "with immediate effect" after China said the man was under investigation over unspecified legal violations and his wife told reporters that he had texted her an image of a knife, leading her to believe he was in danger.
Meng's wife told reporters in the French city of Lyon on Sunday she hasn't heard from her husband since September 25.
Mr Hongwei's wife said she received a message from his phone containing an image of a knife before his disappearance.
In Lyon, Grace Meng spoke to the news media just before Beijing issued its statement, pleading with national governments to intervene, saying she feared that her husband's life was in danger, Agence France-Presse reported.
Grace Meng, left, the wife of missing Interpol President Meng Hongwei, who does not want her face shown, says he last sent her a picture of a knife before falling out of contact in late September.
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"This is the last, last message from my husband", she said.
"I'm not sure what has happened to him", she said.
Meng Hongwei, president of Interpol, gives an address at the opening of the Interpol World Congress in Singapore on July 4, 2017.
She said he was in China when he sent the image.
"This matter belongs to the worldwide community", she told a press conference with her back turned to the cameras out of fear for her safety.
She kept her back turned to the reporters present, and refused to be photographed out of fear for her safety. "For the husband whom I deeply love, for my young children, for the people of my motherland, for all the wives and children, so that their husbands and fathers will no longer disappear".
Asked about the text message Grace Meng received, the French Interior Ministry said through a spokesman it has no information to share.
Meanwhile, Steve Tsang, director of SOAS China Institute in London, stated that due to Meng's stature, the call to detain him must have been taken by someone at the highest levels of the Chinese government.
Meng rose through the ranks of the country's domestic security apparatus when it was under the leadership of Zhou Yongkang, a rival to Xi and the highest-ranking official to be brought down on corruption charges.
Meng's seizure on suspicion of corruption is an ironic reversal for a Chinese official whose ascent to the top of Interpol was supposed to aid Beijing's efforts in catching corrupt runaway officials.