The refurbishment, originally priced at £200m, was won by a Stanhope-led consortium in 1996 but after wrangles over risk allocation, the scheme was thrown out by Geoffrey Robinson, the then paymaster-general, in 1997.
The contract was renegotiated and relet to the Stanhope team in 1999. The consortium also includes Bovis Lend Lease and Foster and Partners.
An NAO spokesman said: "This will focus on how the deal was put together. A lot of such reports try to tease out lessons to learn for the future." The spokesman declined to say whether the report would investigate how the Treasury picked the winning consortium. One insider said: "They are interested in how it's been done as a model of best practice. It's nothing more sinister than that." A Treasury spokesman said the report was a matter for the NAO. He said: "Clearly, the NAO has a remit to examine public projects and we are quite happy for them to do that." The new report follows a report released last week on the £233m Portcullis House project.
It revealed that £13m in compensation had already been paid to contractors after the House of Commons mishandled the awarding of the cladding contract.
An NAO report is also due to be published in the next three months on the first phase of the Channel Tunnel Rail Link.