The Department for Transport (DfT) said the research into the feasibility of a fixed link cost £896,681.
Network Rail chairman Sir Peter Hendy led the investigation, which found that a bridge would cost £335 billion, while a tunnel would require a budget of around £209 billion.
His report concluded that the project “would be impossible to justify” as “the benefits could not possibly outweigh the costs”.
In addition to the huge expense, the inquiry also noted that the necessary work would be incredibly challenging.
The report described how Beaufort’s Dyke – an underwater trench on the most direct route between Scotland and Northern Ireland – would need to be “carefully surveyed” due to a million tons of unexploded munitions being dumped there between the First World War and the 1970s.
Mr Johnson previously talked up the creation of a fixed link but accepted the conclusion of the report.
The research was carried out alongside a wider review of connectivity in the UK, which cost £1,102,525.
The DfT said the total of £1,999,206 for both studies was the amount spent on consultancy fees and department staff costs.
Sir Peter led the review alongside his role at Network Rail, and did not receive additional pay.