GNER was last night told its performance was not good enough after figures showed the number of trains running on time was the worst for five years.
Only 64.9 per cent of GNER trains ran on time between June 24 and July 21, figures from Network Rail show.
It was below the national average of 89 per cent and GNER's poorest performance since early in 2002.
Then, with the rail industry still recovering from crashes at Hatfield and Selby, 69.2 per cent of GNER trains ran on time.
The East Coast Main Line operator said flooding and other problems outside its control caused the delays.
Its performance peaked in the first three months of last year, with 88.4 per cent of trains on time, but performance has steadily slipped.
Guy Dangerfield, of rail watchdog Passenger Focus, said: "Punctuality on the East Coast Main Line has been pretty poor over the last few months, and 64 per cent of trains running on time is not good enough.
"At the end of the day, passengers are not terribly bothered what has caused a delay and what party is responsible for it.
"They are just interested in the industry working together to make it better."
Mr Dangerfield said National Express, which will take over the East Coast line route in December, had promised that 90 per cent of trains would run on time by January 2010, although he said it was a difficult challenge.
A GNER spokesman said only 17 per cent of delays on the East Coast line were within its control.
He said: "We continue to work to reduce these and, in conjunction with Network Rail, the wider issues - such as cable thefts and incidents of trespass on the railway - that are the cause of the vast majority of delays.
"The figures quoted relate to the one-month period up to 21 July, during which parts of the rail network were impacted by the summer flooding.
"Among those most severely affected were lines north of Doncaster, on which services to the North-East run.
"Even after the water had subsided, services were affected while Network Rail carried out repairs."
There was some respite for GNER after Network Rail, which is responsible for the upkeep of the infrastructure on the line, said it was partly to blame
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