According to the UK's Office of National Statistics (ONS), there are around 20,000 Goans holding Portuguese passports who live and work in the UK.
They used their right to freedom of movement within the EU to settle in Britain over the years but now fear their immigration status could change after the referendum on June 23.
"There is a lot of ambiguity. Forget Goans, even British citizens are not clear what a 'yes' or 'no' vote in the referendum would really mean. In the process it causes a lot of concern and unease among Goans who have made the UK their home with their families," Ravi Vaz, president of the Goan Association (UK), told PTI.
Vaz said: "The application process itself involves a large investment of time and money, including translated documents and affidavits. There are many Goans mid-way through this process suddenly left unsure about their future.
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"They may have applied after narrowing down job opportunities here but are now no longer sure what the future would hold in the UK.
"Our message would be to look out for opportunities in the homeland first because the decision to leave your homeland often involves moving entire families. But individual circumstances vary, and if you have decided to make the move, please explore the job market across the EU to see what kind of criteria you meet best.
The EU nationality for some Goans has its roots in the Portuguese colonisation of Goa in the 16th century.
The region was ruled by the European nation for nearly 450 years before it officially became a part of India in 1961.
According to data from the Election Commission of India, 11,500Goanssurrendered their Indian passports in favour of Portuguese citizenship in the five years between January 2008 and January 2013.
(Reopens FGN 16)
The UK has been the first choice for Goans who acquire their Portuguese nationality mainly due to the comfort of the English language and a strong UK Goan community, concentrated largely in Swindon, south-west England, and parts of London.
"Most of the Goans based here are professionals who come with a particular skill set or are entrepreneurs. They have moved here to improve their circumstances and not for the benefits system," said Flavio Gracias, a Goan who has been based in London since 1968.
"In the event of changes following the referendum, they will still be part of the EU and may look at going to Germany or France or other EU countries that have job opportunities," Gracias said.