In a statement on its website, the Central Commission for Discipline Inspection -- the Communist Party's corruption watchdog -- gave no further details of the case involving Ai Baojun, 55, who is also a vice mayor of the commercial hub.
Ai holds the title of director of the Shanghai FTZ, according to his official biography. He has been one of several Shanghai vice mayors since 2007, holding the portfolio for development and planning, it said.
Ai is not the first government official involved with the zone to run afoul of authorities.
Authorities have said that Dai Haibo, previously Communist Party chief and executive deputy director of the FTZ, was under investigation for "severe" violations of discipline and the law.
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Dai was the public face of the trade zone, appearing at news conferences, meeting foreign delegations and running the zone's administration on a day-to-day basis.
Chinese President Xi Jinping has launched a much-publicised drive against corruption after he came to power more two years ago, vowing to target both high-level "tigers" and low-ranking "flies".