The Scotland international was a regular in the side under Pat Fenlon but has played just 32 minutes since Terry Butcher was appointed manager in November.
Thomson said that following the signings of Danny Haynes, Duncan Watmore and Daniel Boateng, as well as the resurgence of Tom Taiwo, he does not expect to figure when he returns to fitness after a calf strain.
However, the 29-year-old, who is scheduled to resume training next Monday vehemently denied his exile is the result of a disagreement with Malpas, as internet speculation has claimed.
Thomson said: "There is no issue with the manager or Mo [Malpas]. I get on really well with Mo.
"I did hear there was something on the internet suggesting Mo and I had a bust-up on the training field. That is laughable to be honest. Liam Craig told me about it - I am not one for Twitter or reading the papers.
"When players are not in the groove and not involved, fans want to know why but there is no reason. The manager picks the team and unfortunately I have not been in it.
"He brought in three players in January. I had limited opportunities before that, so I would imagine my opportunities are going to be even more limited."
Thomson has not given up on earning a place in Butcher's plans. He added: "I am not throwing my toys out of the pram, I am here working hard.
"I have always felt I have the ability to play at the club and fingers crossed I will get an opportunity in the near future. I feel I can contribute a great deal to the team. I will keep working hard to try to push my way into the manager's plans. There have been other boys who have not featured much and then come in.
"Hopefully he will see my quality in training and give me an opportunity to play. I am quite willing to play in the under-20s and East of Scotland League games."
However, Thomson's contract ends in the summer and the former Rangers and Middlesbrough player conceded: "If I am not in the team and not in the manager's plans then of course I would need to look for something else in the summer. That's part and parcel of football."