Labour's Ken Macintosh challenged Sir Peter Housden, Permanent Secretary to the Scottish Government, on why he produced different costings from public spending watchdog Audit Scotland.
Sir Peter was being questioned on the issue by Holyrood's Public Audit Committee for the first time.
Mr Macintosh said: "Half-a-billion pounds is not being reported and, as far as I can tell, you do not provide that information to the committee in a manner that is accessible."
In a report to the committee, Sir Peter said the capital value of the new Forth crossing; the Aberdeen bypass; improvements to the M8, M73 and M74 motorways; improvements to the Edinburgh to Glasgow rail line; and the new Borders railway was £3.28 billion to £3.43 billion.
But Audit Scotland gave a higher estimate for the five projects of about £3.8 billion.
Sir Peter explained this was "essentially the difference between the contract construction costs of the five projects and the figures used in the Audit Scotland report, which include a variety of other costs" such as the purchase of land necessary for works to go ahead. There was no shortfall in funding, he insisted.
The Government has now "undertaken to develop that standardised approach and to review the format and threshold for public reporting of major projects".