The show's right-wing politics shows the colourful steam engines punished if they show initiative or oppose change, the researcher found.
She also highlighted the class divide which sees the downtrodden workers in the form of Thomas and his friends at the bottom of the social ladder and the wealthy Fat Controller, Sir Topham Hatt, at the top.
The criticism, by Shauna Wilton, a professor of political sciences at the University of Alberta, is likely to anger fans of the original books by Rev W. V. Awdry first published in the 1940s which were turned into an animated TV series now shown in 130 countries.
She launched her study after watching the programme with her three-year-old daughter.
She then analysed the plots, characters and other aspects of 23 different episodes to draw her conclusions, which she then presented at a conference of political science in Canada.
She was critical of the fact the show only has eight female characters out of the 49 who feature.
"The female characters weren't necessarily portrayed any more negatively than the male characters or the male trains, but they did tend to play more secondary roles and they're often portrayed as being bossy or know-it-alls," she said.
She also objected to the way the show portrays Thomas, Percy and James slaving away for wealthy bosses like the Fat Controller.
Any attempt to break out of this controlled hierarchy to gain individual power, show initiative or dissent is met with punishment, usually because it goes wrong, she said.
In one episode, Thomas whistles impatiently at a police officer and is replaced with a different engine as a punishment for showing dissent.
"It also represents a conservative political ideology that punishes individual initiative, opposes critique and change, and relegates females to supportive roles," she said. "Any change is seen as disrupting the natural order of things."
But Prof Wilton insisted she show was not all bad, and featured some positive political values like contributing to the community, tolerance of others and good communication.
And she admitted that her three-year-old daughter loves the show and the trains.
Her study shows programmes for children are not as harmless as many parents think if they look more closely, she concluded, and she called for tighter controls of what is broadcast to them.
"We tend to think of children's TV shows as neutral and safe, but they still carry messages," she said.
"Eventually these children will attain full political citizenship, and the opinions and world outlook they develop now, partially influenced by shows like Thomas, are part of that process."
