Whetton is leaving IPC for the second time after rejoining the company to head SouthBank in March 2003. SouthBank managers will temporarily report to IPC chief executive Sylvia Auton.
Whetton worked across a number of IPC divisions in the 1980s and 1990s, rising to publishing director level.
In 1998, he left to become president of OAG Worldwide, the worldwide airline schedules information business, which was owned by Reed Elsevier until last year.
He subsequently become managing director of Raven Fox, the travel and retail division of Euromoney Institutional Investor, then returned to IPC.
BBC Magazines, Conde Nast, Haymarket and the National Magazine Company said they could not comment or had no knowledge that Whetton could be joining them.
News International's recently launched magazine division was unavailable for comment at the time of writing.
However, News International is known to be planning to launch two magazines, called Inside Out and True Lives, into the women's market.
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