The film, directed by Martin Scorsese and starring Willem Dafoe as Jesus who had sexual fantasies about Mary Magdalene, beat Chris Morris's 'Brass Eye' special on media coverage of paedophilia.
The ITC said: "These people, who probably hadn't seen the film at the movies, complained about it in principle."
The showing of the paedophilia special of the cult satire show 'Brass Eye', attracted 992 complaints and Channel 4 was forced to apologise for not giving viewers sufficient warning.
Channel 4 was found to have offended public feeling and failed to provide suitable on-air warnings before the show was broadcast.
Next in line was an episode of 'Spitting Image', which attracted 341 complaints in 1992 over the use of an image of God.
A trailer for Uefa Champion's League coverage, in which a boy misbehaved at the dinner table so he could be sent to his room and watch the football on his TV, also made the list with 233 complaints.
'Living with Michael Jackson' drew 171 complaints, some of which were from the US, and 'Queer as Folk', the racy gay drama following the lives and loves of three gay men in Manchester, had 163 complaints.
Other shows that featured on the list include 'Undercover Britain' and 'The Bill'. The surprise in the list was an episode of ITV's 'This Morning' shown in 2001, which drew 117 complaints because it featured a gay wedding.
The ITC is taken out of service on December 29 and is replaced by Ofcom, the communications industry's new super-regulator.
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