Home Office data published for the first time, shows around 90 people who applied to continue living in the area by September 30 had their application rejected.
Applicants can challenge a negative EU Settlement Scheme application by launching an appeal.
But the3Million, which campaigns for EU citizens’ rights, is concerned about the status of those who are left “in limbo” waiting for their appeals to be concluded.
The EU Settlement scheme was launched in March 2019 to regulate the immigration status of European citizens who live in the UK.
Those who have lived in the UK for five years, and meet the criteria, can receive settled status and remain in the country indefinitely.
Others who have lived in the country for less time can receive pre-settled status, which allows them to remain for a further five years. They can later apply for settled status.
The figures show that since applications opened, 2,830 people applied to continue living in North Kesteven, with 2,650 receiving a conclusion by the end of September.
Of them, 1,880 (71%) received settled status and 630 (24%) pre-settled.
The highest number of applications came from citizens of Poland (750), Bulgaria (420) and Lithuania (420).
Monique Hawkins, policy and research officer at the3million, said many people had lost their job or rental opportunity while waiting for application and appeal outcomes.
She said: “Many people report not being able to get through to helplines, and find it next to impossible to get progress updates on their applications.
“For those who have been refused, the administrative review and appeals process face their own lengthy delays.
“We are extremely concerned about the length of time it is taking to unite people with their lawful status, and thereby their rights to continue living and working in the UK.”
Though the scheme officially closed on June 30, EU citizens with limited reasonable grounds for missing the deadline can still apply to secure their rights.
Around 60 applications were submitted after the deadline in North Kesteven.
The Home Office said people with a pending application, are protected while the outcome of their application is unknown.
A spokeswoman said the EU Settlement Scheme has been an “overwhelming success”, with 6.3 million applications received and 5.5 million people being granted permission to stay so far.
She added: “Caseworkers will always look for reasons to grant rather than refuse.
“Individuals can be refused on eligibility or criminality grounds, and if a refused applicant disagrees with our decision, they can apply for an administrative review or appeal.
“We have published non-exhaustive guidance on reasonable grounds for making a late EUSS application and take a flexible and pragmatic approach to considering them, and we’ve made millions of pounds available in funding for organisations to support vulnerable applicants.”
In a new move, thousands of additional care workers could be recruited to boost the adult social care workforce following temporary changes to the health and care visa to make social care workers, care assistants and home care workers eligible for a 12-month period. This will make it quicker, cheaper and easier for social care employers to recruit eligible workers to fill vital gaps.
The coronavirus pandemic has highlighted a range of staff shortages within the social care sector, placing pressures on the existing workforce, despite the incredible and tireless efforts of social care staff.
This boost follows the recommendation from the Migration Advisory Committee (MAC) to make care workers and home carers eligible for the Health and Care visa and add the occupation to the Shortage Occupation List (SOL).
Inclusion on the Shortage Occupation List will stipulate an annual salary minimum of £20,480 for carers to qualify for the Health and Care visa. The UK is committed to becoming a high-skilled, high-wage economy and the government says minimum salaries must reflect the professional skills that are required to provide quality care. The Health and Care visa will allow applicants and their dependents to benefit from fast-track processing, dedicated resources in processing applications and reduced visa fees.
The temporary measures are expected to come into effect early next year and will be in place for a minimum of 12 months, providing a much-needed staffing boost while the sector deals with the additional pressures of the pandemic, at which point they will be reviewed.