The 39-year-old hunk created Taboo Productions Ltd to handle the finances for the eight-part series, which he wrote, produced and starred in - but his first solo venture has transpired to be a financial flop.
A source said: "These new figures will make stark reading for Tom.
"No matter who you are or how much money you're worth, £2 million is a lot of money to simply throw away.
"This is the first major TV drama Tom has overseen himself. He has written it, produced it and starred in it, so he was always going to come up against some difficulties."
Accounts show that Tom spent as much as £10.4 million on 'Taboo', while its income reached £8.4 million, meaning Tom took a sizeable financial hit on making the show.
However, the Hollywood star still hopes to recoup more money through DVD and digital sales, while he can also sell the rights abroad.
The source told The Sun newspaper: "Tom will hope to eventually make the money back through DVD sales, downloads, streaming and syndication rights.
"As well as being aired in the UK and in the US, 'Taboo' has already been sold around the world in the likes of Spain, Portugal and Russia."
Tom came up with the idea for 'Taboo' along with his dad Edward 'Chips' Hardy, and Sir Ridley Scott agreed to direct the project after the BBC purchased the rights.
Although the show has proven to be a financial flop thus far, plans are already in place to make a second series.
The drama has attracted relatively modest viewing figures, but is actually among the most-watched shows on the BBC iPlayer, the broadcaster's catch-up service.