Network Rail apologized and said the problem had been caused when the power supply to the signals failed.
Two rail companies earlier warned passengers to avoid travel if possible.
Great Northern and Thameslink urged customers not to make any trips during the morning unless “absolutely necessary”.
Network Rail’s East Coast Main Line director Paul Rutter said teams were investigating what had happened and “early feedback from the site indicates that the engineering work carried out over the weekend may have been involved”.
“I know how important a reliable train service is to passengers and freight. I am sincerely sorry for the disruption we caused,” he added.
National Rail Enquiries said that disruption on Great Northern and Thameslink trains was expected until about 17:00, with some cancellations and delays.
Grand Central, Hull Trains and LNER had also been hit by the problem but are no longer affected.