NR had admitted breaching health and safety regulations in the May 2002 Hertfordshire disaster.
Its predecessor company Railtrack was the infrastructure company in charge at the time of the crash but NR has shouldered the responsibility.
The prosecution, at St Albans Crown Court under the Health and Safety at Work Act, was brought by the Office of Rail Regulation (ORR).
The now in-administration maintenance company Jarvis, which was responsible for the section of track at Potters Bar, also faced prosecution but the ORR decided in March not to proceed as the prosecution was "no longer in the public interest".
The sentence against NR was imposed by Judge Bright QC after Nicholas Hilliard QC, appearing for ORR, had said the poor state of a set of points on the track at Potters Bar had made the crash "inevitable".
Six passengers - Austen Kark, Emma Knights, Jonael Schickler, Alexander Ogunwusi, Chia Hsin Lin and Chia Chin Wu - were killed in the crash on May 10 2002.
They were on a West Anglia Great Northern express train travelling from London to King's Lynn in Norfolk which derailed at a faulty set of points just outside Potters Bar station.
The seventh victim was Agnes Quinlivan, 80, who was walking nearby and died after she was hit by debris.
All those killed were in the train's fourth carriage which became airborne after derailing and ended up getting wedged under the canopy of Potters Bar station.
NR is a not-for-dividend organisation, with no shareholders and with its debt guaranteed by the Government.
This means that any fine imposed on the company effectively comes out of the public purse.
Speaking after the court case today, Perdita Kark, the daughter of Austen Kark, said: "It's offensive that I pay a fine for something that killed my father.
"Directors of the two companies should have been in the dock as individuals and they should have paid out of their own purses."
Ms Kark, whose mother, author Nina Bawden, now 86, was badly injured in the crash, added: "This fine is going to be paid by the taxpayer and will mean there is less money to be spent on the rail network.
"The crash has made my mother's old age desperately difficult."
NR admitted failings over the installation, maintenance and inspection of adjustable stretcher bars which keep the moveable section of a track at the correct width for train wheels.
The ORR brought the prosecution after the jury at the long-awaited inquest into the crash in July last year found that unsafe points caused the accident.
Director of rail safety at ORR Ian Prosser said: "Today marks the end of a long process in which we have sought to gain a sense of justice for the families of the victims of the Potters Bar derailment.
"It is welcome that Network Rail, as the successor to Railtrack, pleaded guilty to health and safety breaches, demonstrating that, under its new management, it is now an organisation willing to take responsibility and learn from past mistakes.
"Safety on Britain's railways has improved significantly over the last nine years and, today, statistics show we have one of the safest railways in Europe.
"But there can be no room for complacency. The safety culture of the rail industry can be significantly strengthened.
"As long as the regulator continues to have to step in to enforce improvements or bring prosecutions where things have gone wrong - as we have done many times this year - then, despite progress, it is clear that the industry has significant work still to do."
A Network Rail spokesman said: "This week marks the ninth anniversary of the terrible, tragic event at Potters Bar. We recognise for many that the sorrow remains and we should all pause and reflect as we remember those who lost their lives.
"We have today been sentenced for failings that contributed to this accident and we accept the fine as we accept the liabilities inherited from Railtrack. We say again today that we are truly sorry."
The spokesman went on: "Private contractors are no longer in control of the day-to-day maintenance of the nation's rail infrastructure since NR took this entire operation in-house in 2004.
"Today the railways are safer than they have ever been, yet our task remains to build on that record and always to learn any lessons we can to make it ever safer for passengers and those who work on the railway."
Keith Norman, general secretary of train drivers' union Aslef, said: "It is ludicrous that six people died but the managers responsible for rail safety walked away unscathed - while the public picks up a 3 million bill.
"Surely those individuals responsible should be punished - not the travelling public?"