Beijing said he was under investigation by the country’s anti-corruption body for unspecified breaches of the law.
Mr Meng, also a vice-minister of public security in China, was reported missing after travelling from the city of Lyon in France, where Interpol is based, to China on 25 September.
Interpol said it had received his resignation from the presidency on Sunday with immediate effect.
China’s National Supervision Commission, which handles corruption cases involving public servants, said Mr Meng was under investigation in a statement on its website.
Mr Meng is the latest high-profile disappearance in China, where a number of top government officials, billionaires and even an A-list celebrity have vanished in recent months.
Earlier this week, actress Fan Bingbing, who disappeared in China in July, emerged with a public apology and a fine of 883 million yuan ($129m; £98.9m) for tax evasion and other offences.
What has Interpol said?
In a statement on its Twitter site, it said it had received the resignation with immediate effect.
Under its terms it has appointed senior vice-president Kim Jong-yang of South Korea as acting president.
A new president will be elected for the remaining two years of Mr Meng’s mandate at the general assembly in Dubai next month.
On Saturday, the international police agency had urged China to clarify Mr Meng’s status, saying it was concerned about the well-being of its president.
France has opened an investigation but said on Sunday it had no further information.
What did Mr Meng’s wife say about his disappearance?
Image copyrightAFPGrace Meng, speaking shortly before China’s confirmation of the detention, told journalists she thought he was in danger.
She issued an emotional plea for international help to find her husband.
On the day he went missing, she said he had sent her a social media message telling her to “wait for my call”, before sending a knife emoticon, signifying danger.
“I’m not sure what has happened to him,” she said.
With her back to the cameras to avoid being identified out of fear for her safety, she held back sobs to read out a statement in Chinese and English.
“We are always connected by hearts. He would support me in doing this. The matter belongs to fairness and justice. The matter belongs to the international community. The matter belongs to the people of my motherland.”
The Xi campaign
Analysis by Hugh Schofield, BBC News, Paris
The Chinese authorities have confirmed what everyone already presumed: that Meng Hongwei was detained when his plane landed in China.
The fact that news of his detention was released by Beijing’s anti-corruption authority suggests Mr Meng has been caught up in the broad anti-corruption campaign ordered by President Xi Jinping, and which has already led to the disappearance of many senior figures.
The mystery of what happened to him has now been cleared up – but the details of the charges weighing against him, and the fate that awaits him are as opaque as ever.
What does Interpol do?
Interpol co-ordinates searches among its members, issuing yellow notices for missing persons and a red notice – an international alert – for a wanted person. However, it does not have the power to send officers into countries to arrest individuals or issue arrest warrants.
It is Interpol’s general secretariat that largely oversees the day-to-day work of the 192-member organisation, with the role of the president largely ceremonial.
Who is Meng Hongwei?
Image copyrightAFPHe was elected Interpol president in November 2016, the first Chinese to take up the post, and was scheduled to serve until 2020.
He headed the organisation’s Executive Committee, which provides overall guidance and direction.
Mr Meng has 40 years of experience in criminal justice and policing in China, notably in the fields of drugs, counter-terrorism and border control.
After his election human rights groups expressed concern that the move could help China pursue political dissidents who have fled the country.
