Previously, the estimate to electrify the railway line between Cardiff and London had been £874m in January 2013, which rose to £1.5bn in September 2014.
However, CEO Mark Carne told the House of Commons public account committee how "inadequate planning and scope definition" in the projects early stages along with an out-of-date cost base had resulted in the price increases.
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"From the very early stages of the design of a project, as you go forward there's a significant degree of uncertainty," Mr Carne told the committee.
Committee chair Meg Hillar called the increase "staggering".
"It's unbelievable and it's unacceptable that there was such poor planning," she added.
Mr Carne and DfT Secretary Phillip Rutnam also told the inquiry that it was likely the Great Western project would not meet its expected completion date of 2018.
(LM/CD)
