The track operator was fined a record £14M by the Office of Rail Regulation (ORR) in February for delays of up to four days following engineering overruns at Liverpool Street, Rugby and Shields Junction following the New Year holiday.
As little as half the number of qualified workers had been found to complete overhead line work during the New Year, causing significant delay.
Network Rail said this time it had used a "Gold Command", or emergency strategic command post, to direct operations and ensure train movements were not disrupted when services resumed on Tuesday.
The ORR had recommended extending the "Gold Command" structure to push works through more quickly in its report into the New Year overruns .
"We normally use this type of arrangement when there is a major incident," said a Network Rail spokesman.
"During the New Year delays, when we set-up the Gold Command, it drove the works through much more quickly. It allows us to monitor work virtually minute-by- minute.
"In this instance we decided we would establish the Gold Command before work started, and it seems to have been successful."
Train operator National Express claimed a delay on the line at Shenfield in Essex was due to the Easter work. Passengers were left stranded early on Tuesday morning as a signal failure at Shenfield disrupted services between London and Ipswich, Colchester and Southend, between 5.30am and 8.40am.
Network Rail said National Express's comments were 'misleading', and points were replaced at one end of the platform at Shenfield over the Easter break, but when services resumed on Tuesday morning there was a fault at a different set of points at the other end of the platform which caused the signal to fail.
Network Rail did admit to one minor overrun at Crewe, not on the West Coast Main Line. This caused the cancellation of three early trains.