Figures show there has been a sharp drop in nurses registering with the Nursing & Midwifery Council since the EU referendum.
In July 2016, 1,304 nurses from the EU joined the Nursing and Midwifery Council register, compared to 46 in April 2017 - a fall of 96%.
It comes as the NHS is already struggling with nurse vacancies and, without this supply line, shortages are likely to get worse.
Research by the Royal College of Nursing (RCN) found one in nine posts in England was vacant and claims the NHS is short of 40,000 nurses.
Anita Charlesworth, Director of Research and Economics at the Health Foundation, said; "Without EU nurses, it will be even harder for the NHS and other employers to find the staff they need to provide safe patient care. The findings should be a wake-up call to politicians and health service leaders."
A Department of Health (DoH) spokeswoman said EU nurses played a "valued" role in the NHS and they would be a priority in Brexit negotiations.
Overall there are 650,000 nurses on the NMC register with just over 36,000 of these having trained in the European Union.