The rail regulator has rejected Network Rail's proposal to spend £14 million on improvements and will fine the company instead, after an engineering overrun caused travel chaos in January.
Network Rail appealed the £14 million penalty imposed by the Office of Rail Regulation (ORR), claiming the fine was "unnecessary and excessive" and proposed spending the money on a series of improvements instead.
Passenger Focus, train operators and others, supported Network Rail's proposed alternative to a fine.
However, the watchdog found "serious weaknesses" in Network Rail's planning and execution of the work, and decided the fine would stay.
ORR chief executive Bill Emery said: "The board considered the representations very carefully. We remain convinced the systemic weaknesses we have found in Network Rail's approach to the planning and execution of its engineering work are a serious and continuing breach of its licence meriting a financial penalty.
"We consider that to accept Network Rail's proposal to mitigate the fine in its entirety would reduce the effectiveness of the incentive that penalties place on the company to secure compliance with its licence. We are therefore confirming the penalty of £14 million."
Consumer action group Passenger Focus said it was disappointed by the decision.
Chief executive Anthony Smith said: "Passengers will be extremely disappointed the ORR and Network Rail could not come to a sensible compromise.
"Passenger Focus brokered a package of passenger improvements, mainly focused on boosting the quality of passenger information, which would have meant some benefit reached passengers from this regulatory action.
"Now £14 million of extra investment has been lost to passengers. Instead of a sensible discussion, the posturing by the ORR and Network Rail has resulted in the Treasury benefiting, not passengers. This is not the joined up railway and thinking that passengers expect and deserve."
Passenger Focus had suggested a number of improvements that would benefit those using west coast mainline stations, including better information screens, improved waiting areas and maintaining mobile phone signals through tunnels.