The first search was made minutes before he saw the magistrate, and the second made by jail officers of the New South Wales Corrective Services.
"The first search which was one that I totally understand is about making sure that you don't have anything that you could self-harm with and strip search just absolutely threw me," he told ABC.
While NSW Premier Barry O'Farrell defended the strip search as a standard police procedure, Mr Thomson insisted two rounds of stripping naked in front of jail guards was not routine.
"You take off an item at a time and turn around until you have nothing on . . . so that was both distressing and humiliating," Fairfax Media quoted the MP.
"(I feel) both angry and humiliated, which I think at least the latter was the intention of the strip search. There is no other possible explanation for it," he added.
Mr Thomson, who is scheduled to appear before a Melbourne court on Wednesday, Feb 6, denied charges of misusing Health Services Union (HSU) funds and engaging the service of a prostitute.
The 150 charges will be laid against him, which he said could have been done minus the fuss his arrest and strip search created.
In 2012, Mr Thomson said someone used a phone in a hotel room hired in his name to call escort services as well as a credit card with his signature. The credit card was slipped back in his wallet, the MP claimed.
Dropped like a hot potato by Labor when questions about the party paying for his legal fees for the HSU charges cropped up, Mr Thomson is now being blamed by Communications Minister Stephen Conroy for the party's recent poor performance in opinion surveys.
Newspoll showed a 56-44 per cent result in favour of the Coalition under a two-party preferred basis, while the Galaxy survey yielded a 54-46 per cent result.
Besides Mr Thomson, Mr Conroy also blames Liberal-run state governments for dragging down the national economy.
"We're focused . . . (but) we've got those deadweights of the Victorian government that's dragging the state back, the Newman government which is dragging the Queensland economy backwards. Cutting is in the Liberal party's DNA, and they will do that if they win federal government," Mr Conroy was quoted by Skynews.
Since his ouster from Labor, Mr Thomson had to shoulder the cost of his legal battles, and he said that he risks losing his home to pay his defense team.
"You're talking hundreds of thousands of dollars, you're not talking a few thousand dollars. It's significant money to defend yourself," he pointed out.