The campaign, using the slogan "Bigger. Fatter. Gypsier." over images of Gypsy boys and girls, triggered 372 complaints and a protest at Channel 4's London headquarters.
The Advertising Standards Authority (ASA) had initially said that it would not probe the adverts as they were 'in keeping' with the tone and content of the hit series.
In a judgement earlier in the year, the ASA said that the ads "might not be to everyone's taste", but they were unlikely to cause serious or widespread offence.
However, the ASA has now changed its position following a request by the Irish Traveller Movement in Britain.
The regulator took the recommendation of its independent review council that its original judgement was "flawed" and a formal investigation was required.
In a statement, the ASA said: "In their evaluation, the council noted that it had made its original decision without the benefit of knowing that the Irish Traveller Movement of Britain had complained and that this was a material fact to which they should have had regard."
Yvonne MacNamara, the director of the Irish Traveller Movement in Britain, said that the decision marks a "great victory" for travellers and gypsies, which "may prove a turning point as to how travellers and gypsies are portrayed in the media".
"Channel 4 has made a fortune out of their documentaries, which many travellers and gypsies believe have invaded and misrepresented their lives," she said.
"We hope this decision may herald an end to the negative caricaturing of travellers and gypsies in the wider media."
Channel 4 and Honda UK, the sponsor of documentaries on Channel 4, each said: 'We will await the outcome of the investigation'."