The countries with the most applicants were Poland with 347,300, Romania (280,600), Italy (200,700), Portugal (162,500) and Spain (115,700).
Launched in March, the online system allows EU, wider European Economic Area and Swiss citizens residing in Britain to obtain, free of charge, settled status or pre-settled status.
They have until December 2020 to apply.
The figures are provisional, but show the surge in applications in September as the Brexit deadline approaches.
Britain is due to leave the European Union on October 31, without a divorce deal unless an agreement or a third delay can be negotiated in the remaining three weeks.
Nicholas Hatton, who founded The3Million, which campaigns for the post-Brexit rights of EU citizens in Britain, said the spike reflected heightened worries among Europeans.
"When you frighten people, they get worried and they try to guarantee their status, and the government has really scared them with the risk of no deal," he told AFP.