Meng Hongwei's wife reported him missing on Friday, the official said.
"Interpol is aware of media reports in connection with the alleged disappearance of Interpol President Meng Hongwei".
Before taking over at Interpol, Meng Hongwei was deputy minister in charge of public security in China.
Hong Kong's South China Morning Post quoted an unnamed source as saying Meng, 64, was under investigation in China and had been taken away for questioning as soon as he landed there.
Presidents of Interpol are seconded from their national administrations and remain in their home post while representing the worldwide policing body.
Rights groups previously said that Beijing could use Meng's position to arrest and deport its critics overseas.
Beijing has in the past pressed countries to arrest and deport to China citizens it accuses of crimes, from corruption to terrorism. His wife and children live in Lyon, reports Europe 1.
Interpol president has been reported missing after travelling to his native country China.
"Interpol's General Secretariat headquarters will not comment further", it said.
But rights groups warned of possible abuses.
While there are no public allegations against him, Meng, a member of the ruling Communist Party, likely worked closely with former security chief and Politburo Standing Committee member Zhou Yongkang, who is now serving a life sentence for corruption.
Xi has also placed a premium on obtaining the return of officials and businesspeople accused of fraud and corruption from overseas, making Meng's position all the more sensitive.