The two were Gerald Marie, president of Elite Europe, and Xavier Moreau, president of Elite Model Look. Mr Marie was filmed propositioning the investigator Lisa Brinkworth when she posed as a model in Tuesday's programme, screened on BBC1 as part of the MacIntyre Undercover series.
Mr Marie also told Donal MacIntyre, posing as a photographer, that he planned to seduce finalists from the Elite Model Look contest, whose average age is 15, said the BBC.
Elite, which represents Naomi Campbell and Cindy Crawford, launched an investigation and on Wednesday the chairman, John Casablancas, said several executives had been suspended and ordered to explain themselves.
In a statement he offered an "unreserved apology" for the behaviour displayed by his staff in the film on what he called "some of the darkest aspects of the modelling industry".
The film also included evidence that men employed to ferry young models around were forcing drugs on them without the knowledge of the agencies involved.
Elite said Mr Moreau would be replaced by Thierry Grin, a Swiss attorney with the company in New York, and that Mr Marie's replacement would be announced soon.