Two million EU citizens living in the UK have been granted settled status - allowing them to remain here permanently after Brexit.
Another 4,600 applications were refused, 36,500 were withdrawn and 34,900 were made by people who are not eligible for the scheme.
In response to the figures, the Liberal Democrats called for EU citizens to be automatically given a right to stay.
They say there is a risk of "a new Windrush-style scandal."
The Windrush scandal meant some British citizens from Commonwealth countries were unable to prove their right to be in the UK, leaving them without work and access to benefits - and leading, in some cases, to people being wrongly deported.
The party says successful settlement scheme applicants should be given physical documented proof of their permanent leave to remain, to avoid them experiencing similar problems.
But the Home Office said an automatic system could lead to confusion and lead to EU citizens struggling to prove their status in years to come.
The figures also show that a further 1.5m people, who have been in the UK for less than five years, have been given pre-settled status.
They can apply for permanent residency when they pass the five year threshold. Both pre-settled status and settled status mean people can work, study, receive healthcare and access benefits and services as they do now.
'Windrush on steroids'
EU citizens have until 30 June 2021 to apply for the settlement scheme, which is operated by the Home Office. The scheme is designed to give EU citizens - who entered the UK under the terms of the EU's freedom of movement principle - the right to remain in the UK after Brexit.
Applicants have to prove they have already been living in the UK for five years (or less for pre-settled status). Downing St has said those who fail to apply by the deadline will not face automatic deportation.
However, those granted settled status do not receive any physical documentation as proof of status. The Home Office has previously said that successful applicants can print their digital confirmation letter, but this cannot be used as evidence of settled status.
The Liberal Democrats' home affairs spokeswoman Christine Jardine said millions of EU citizens in the UK have been "living under a cloud of uncertainty."
She said the figures for pre-settled status and rejected applications show the "scheme is anything but automatic."
"And without physical proof of their rights, EU citizens will be at the mercy of the Conservatives' hostile environment. They must not become the victims of a new Windrush-style scandal," she added.
The3million, a campaign group representing EU citizens in the UK, echoed the warning, citing the potential for a "Windrush on steroids" if EU citizens' right to remain is not "enshrined in legislation."
The Home Office said it understood the attraction of a physical document, but in the long-term these can expire or become invalid. Physical documents can also be lost, stolen or tampered with, it said, adding that people already use digital services for banking, accessing benefits and paying taxes.
Immigration minister Kevin Foster said EU citizens were an "integral part of UK society" and 3.5 million had already secured their rights in UK law.
He said there is "plenty of time left to apply" before the deadline, adding that there is "a wide range of support is available online, over the telephone and in person if you need it.