The British government is unlikely to be able to replace European funding in Northern Ireland, the Institute of Directors (IoD) said.
Economic growth inspired by a future reduction in corporation tax on businesses may slowly close the gap, the influential organisation of business leaders added.
It gave evidence to the Northern Ireland Affairs Committee of MPs which is investigating the impact of a Brexit.
The lobby group said: "Given the level of support that Northern Ireland receives from Treasury and the contribution that we have received and continue to receive from Europe - peace funding, agriculture support, Interreg and research etc - we believe it unlikely that the UK government will be able or willing to replicate funding to the same degree, especially when the chancellor is still cutting back public expenditure.
"Given time and a reduction in corporation tax supplemented by other measures, economic growth here might help to close the gap but it could take a considerable time to do so."
Brexit campaigners have claimed Northern Ireland got back £67 million less than it contributed to Europe last year.
A snap UK-wide IoD survey following the British prime minister David Cameron's agreement with the EU earlier this year showed that 60 per cent would vote to remain in the EU and 31 per cent would vote to leave.
A Northern Ireland survey showed that closer to 75 per cent of respondents would prefer to stay in.
The IoD as an organisation is neutral but said only a fraction of listed company boards were discussing the risks associated with Brexit.
It warned: "The uncertainty as to the outcome of the referendum presents a real challenge.
"Running a business is inevitably risky and managing risk is an ongoing issue for leaders. Any uncertainty makes it difficult for them to plan ahead.
"In the event of an exit vote, uncertainty will continue until there is clarity on the way ahead."
It said EU employment and social policy was unhelpful to business, and European Court of Justice rulings on areas like holiday pay calculation made employment law complex.
However, it said the EU was a significant market for its members, two thirds who responded to a recent survey traded in or with the EU and nearly half imported goods from the union.
A quarter of businesses benefited directly from EU funding and nearly half employed EU nationals from outside the UK.
