The fantasy political drama, Nua Mek, about a fictitious prime minister controlled by an evil sorcerer, was axed just hours before the final episode of the second season.
Channel 3 declared the episode socially divisive and says it made the decision without government interference.
Freelance Thai journalist Saksith Saiyasombut says there's been a big backlash on social media.
"It shows that there can be political controversy made from very small things, and the outcry about the cancellation of this series is one indication of that," he said.
"Now, the thing is, how real of a political scandal it is, with actual political consequences, is still yet to be seen."
One theory behind the show's cancellation is that it was seen to parody the relationship between current prime minister, Yingluck Shinawatra, and her brother and exiled former PM, Thaksin Shinawatra.
Government critics argue that Mr Thaksin still controls his sister, and the sorcerer on the TV series symbolises that relationship.
Dr Nicholas Farrelly from the Australian National University says many Thais may make a more literal interpretation.
We've had all sorts of talk over the years that Thaksin has perhaps dabbled in various darker arts...the reality is that most Thais are quite accepting of the fact that there are other powers that exist our universe.
ANU researcher Dr Nicholas Farrelly
"Among Thailand's political elite there continues to be a pretty significant strain of superstition," he said.
"We've had all sorts of talk over the years that Thaksin has perhaps dabbled in various darker arts that are available to those with the appropriate training and insights.
"That's usually dismissed as yet another effort to diminish his status in the eyes of his supporters, but the fact that the reality is in these kinds of cases is that most Thais are quite accepting of the fact that there are other powers that exist our universe."
The opposition Democrat Party says it suspects the government had a hand in getting the show axed.
Party spokesman Isra Sunthornvut wants the broadcast authority to explain the situation.
"What we did, and what we are doing - or planning to do - is to send a formal complaint to the NBTC, which is the national broadcasting telecommunications committee, to see if there is any government tampering," he said.
"If there is any signs or evidence of government tampering then it can bring charges against the government itself."
The National Broadcasting Commission has announced that it will investigate the axing of the program, but journalist Saksith Saiyasom accuses the opposition of hypocrisy over its demands.
Most of this controversy doesn't come from the fact that this particular soap opera has been cancelled, but rather...that censorship and media interference from politicians is still there.
Freelance Thai journalist Saksith Saiyasombut
"Most of this controversy doesn't come from the fact that this particular soap opera has been cancelled, but rather one of the bigger pictures is that censorship and media interference from politicians is still there," he said.
"And the opposition should be looking at themselves in the mirror, because when they were in government they did a huge degree of political interference as well."
If there was government intervention, it certainly wouldn't be the first time a production's been censored due to political sensitivity.
Dr Farrelly says in April, a film adaptation of the Shakespeare play Macbeth was banned because it would also cause division.
"Sad to say that at this point in the nation's history there are many people who are motivated to clamp down on anybody who they feel is presenting materials which are detrimental to their side of politics," he said.
"It strikes me that while Thai society can't accept such fictionalised portrayals of various political activities, then there's no way it's going to deal with the very real challenges that it faces here in the real world, and not the world on the TV."