John Peto, Director of Education at the Nerve Centre in Derry, said enquiries from partners across Europe have already stopped since the Brexit vote.
The insitute, which relies on European Peace funding, may not receive the same amount of money when power is transferred fully back to the UK.
Speaking to BBC Radio Foyle, he said: “It has enable us to innovate and to take risks with projects and to gain new learning that otherwise might not have been possible with the need to play safe with public money.
“It also allows us to work with international partners, local funding often doesn’t give you that opportunity.
John Peto claimed the institute has already been impacted by Brexit
“Throughout the history of the Nerve Centre we have worked with a range of European projects that have seen us work with partners across Europe and across the world too.
“One very concrete outcome already is that we noticed is that we would be contacted regularly by organisations across Europe looking for partners in European projects.
“We have a strong track record on delivering on those projects so they come to us to see if we will partner with them.
“Those calls I would have previously been dealing with, one or two enquiries a month, from people looking to partner with us on various projects that would tie in with our work. Now it is nearer to one every three months and very few calls, very low interest.”
The rest of Europe sees the UK as maybe a pariah state
The Northern Ireland Peace programmes were set up to promote economic and social progress in Northern Ireland and the Republic of Ireland on the border.
Get Quotes on Home Insurance
Mr Peto suggested that the rest of Europe have changed their opinion when thinking of partnering with the UK.
He added: “The rest of Europe sees the UK as maybe a pariah state.
“Or maybe the flux and uncertainty around it, why would they partner with a UK partner? If they don’t have to.
In pictures: Theresa May meets with EU's Tusk Thu, April 6, 2017
The two leaders held talks on Brexit negotiations
AFP/Getty Images 1 of 9
European Council President Donald Tusk gestures to members of the media as he leaves 10 Downing street after talks with British Prime Minister Theresa May in central London
“That partnership may not come through, they may never deliver and the UK may be out of Europe before the project gets off the ground.”
The Director of Education finished by arguing that he didn’t think the institute would receive the same amount of funding after Brexit, despite assurances made to him from Theresa Villiers, the Secretary of State for Northern Ireland at the time.
“I don’t believe that a British government in Westminster, funding for organisations in Northern Ireland… I would be really concerned that even if there is a benefit to the British exchequer from leaving Europe, which I absolutely don’t know, I don’t think those benefits will be felt by us in Northern Ireland.”