A poster for conference call firm Powwownow shows a man on an underground train surrounded by zombie-like characters in masks.
Changing Faces says the adverts are "insensitive" because of the similarity to masks worn by people recovering from burns.
Powwownow says the images are not targeting those with facial disfigurements and instead show characters from "fantasy horror".
In one advert, a woman is shown in the middle of a group of people wearing masks similar to that of Jason, the main character of the Friday The 13th movie franchise.
In a blog post, Changing Faces chief executive, James Partridge, said the tagline of the campaign - Avoid the Horror - was "disturbing".
He wrote: "It reinforces the harmful association that people who wear masks as part of their treatment and who have burn scarring, are to be feared and avoided."
Changing Faces says Powwownow originally agreed to take down the adverts.
In a statement to Newsbeat, a spokesman from the conferencing service said: "When we received a complaint from Changing Faces, we pulled the advert as a mark of respect to the charity's perspective and undertook a review of the advertising strategy.
"After this robust review, we reinstated the advert as a reflection of our belief in the creative concept, its clear reference to the fantasy horror genre and the fact that we are in no way targeting or discriminating against people with facial disfigurement, or indeed any people.
"The adverts focus purely on the horror of the commuting experience and in no way target any individuals."
Catrin Pugh from Wrexham sustained burns to her face and body when the coach she was travelling in crashed in France in 2013.
She's been undergoing treatment ever since.
Speaking to Newsbeat, she said: "Wearing my compression mask is why my face looks 'normal' and was one of the most important parts of my treatment.
"This advert, suggesting people in masks are 'horrors' makes me so angry."
"I remember when I first went out into the public wearing my mask, and due to my eyesight I couldn't see it, but my sister said almost everyone turned and gawped.
"If that is then associated with being like a horror, as the advert suggests, it could have been far worse, with hurtful reactions, rather than curious reactions which is what I received."
Powwownow insists that the characters in its campaign are "commonplace in the world of computer games, TV, entertainment and film.
"We wish to reiterate that there is absolutely no intention to offend anyone at all."
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A charity has criticised a series of adverts which it claims are offensive to people with facial burns.