Home Office data, published for the first time, shows around 180 people who applied to continue living in the area by September 30 had their application rejected.
Applicants can challenge a negative EU Settlement Scheme decision by launching an appeal.
But Monique Hawkins, policy and research officer at the3million, which campaigns for EU citizens' rights, 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.
"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."
The EU Settlement scheme launched in March 2019 to regulate the immigration status of European citizens who live in the UK.
Since applications opened, 12,400 people applied to continue living in Aberdeenshire, with 11,880 receiving a conclusion by the end of September.
Of them, 8,280 (70 per cent) received settled status and 3,130 (26 per cent) pre-settled, allowing them to remain for a further five years.
The highest number of applications came from citizens of Poland (4,320), Lithuania (2,480) and Latvia (1,480).