The organisation was created as part of the Government's pension reforms.
Tim Jones, the chief executive of NEST, said it was great news for savers that with over three million workers having been automatically enrolled workplace pensions are becoming the norm.
He said: "Having grown from a few hundred members to 1 million in under 2 years, NEST is proud to play our part in ensuring automatic enrolment is a success.
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"Reaching this milestone is an important moment for us, but there's a lot more to do to make sure the millions due to be enrolled get a helping hand to save for their future."
Pensions Minister Steve Webb said: "Automatic enrolment is a stunning success and more than 3 million people are now saving in a pension for the first time or saving more, reversing decades of decline and creating a new generation of savers.
"This is a landmark achievement.
"NEST has a pivotal role in helping millions save for a more prosperous retirement."
Nigel Sanders, financial director of Fluidata, whose members took part in an event to mark the milestone, said: "I believe it should be every company's responsibility to help staff secure their futures.