The rail regulator has hit back after being criticised by transport minister Kim Howells.
A review of the railways is due to report its findings
Dr Howells told the Financial Times it was "insane" Tom Winsor, not the Transport Secretary, Alistair Darling, decided how much was spent on railways.
He added a boost of £22.3bn over five years for Network Rail announced by Mr Winsor in December caused the transport department "enormous difficulties".
But Mr Winsor told BBC Radio 4's Today programme Dr Howells was "criticising a system that in reality does not exist".
Decisions on transport planning and spending were for government - "if it has the political courage to make them", Mr Winsor added.
"It is for the regulator to translate those decisions into the kind of network we need to have."
But government could not and should not be able to "year by year turn the funding up or down according to political priorities", Mr Winsor told Today.
"Political horizons are considerably shorter than transport planning ones," he added.
"Transport planning cannot be done on an annualised basis - that is what crippled British Rail for 50 years during nationalisation," Mr Winsor told the programme.
Mr Howells has a reputation as an outspoken minister
Some politicians "would love to go back to the days of nationalisation - of patchy rail maintenance, poor performance, monopoly abuse and much else besides", he added.
Dr Howells told the FT the whole structure of Britain's railways needed a radical overhaul to tackle "crazy" bureaucracy, and the government wanted to tighten its grip on the way the industry was run and regulated.
But Mr Winsor told Today the system was coherent and rational - but government was failing to play its part.
"You cannot have 100% of the existing network for 50% of its efficient cost," he added.
"That is why independent regulation exists - to compel the participants in the system to be honest and realistic."