"The message reveals a significant, but now overlooked event that occurred virtually 100 years to the day of the start of the trial," Smith said in a statement.
He was referring to Adm. Jackie Fisher's development of the battleship HMS Dreadnought, which was launched in February 1906, the BBC said.
Smith said it took him a total of about 80 minutes to work out the code and hide it in his text.
He earlier said he decided to create the secret message as a "matter of fun."
In the decision, Smith ruled Brown did not lift material from "The Holy Blood and the Holy Grail" for his breakout best-seller.
Director Ron Howard's film version of "The Da Vinci Code" opens worldwide May 19.