Network Rail has been fined £2.4 million after the railways watchdog found it had committed a "moderately serious breach" of its network licence.
The station and track operator was found to have failed to plan for an overrun of a resignalling scheme in the Portsmouth area which, the Office of Rail Regulation (ORR) said, affected many passengers.
Warning that similar future breaches would result in further fines, ORR chief executive Bill Emery said the penalty would provide a "strong incentive" for the company to conduct stronger risk assessments in future.
"We consider that a £2.4 million fine is proportionate for this breach and is in line with our policy. We also consider that imposing this fine will reinforce the requirement that Network Rail must meet its commitment to apply fully the lessons it has learned here to future decisions," he explained.
The group's infrastructure director, Peter Henderson, said he was "very disappointed" by the regulator's decision to impose a fine.
"The company took prompt action to mitigate the disruption to passengers and the majority of services were restored some time ago," he explained.
Mr Henderson added: "We will continue to work with train operators to manage delivery of these major renewal and remodelling projects in an affordable way to achieve improvements for passengers and freight users, the vast majority of which are delivered on time and on budget."