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Leaving the EU could leave a question mark over millions of pounds the county council is relying on to fund dozens of schemes aimed at boosting jobs and investment.
Kent County Council says the Brexit vote could jeopardise funding for existing programmes and leave the county isolated when it comes to getting funding for new ones.
Cllr Mark Dance, KCC cabinet member for economic development, said he could not guarantee that a target to secure £100m from the EU would be met.
To date, Kent has seen £52m ploughed into various schemes for the period 2014 to 2020 - a little over half the sum it hopes will come its way.
Among the beneficiaries are the Port of Dover, which has been allocated £42.3m under an EU programme called Connecting Europe Facility.
Cllr Dance said funding could be withdrawn early from some schemes if the government negotiated an agreement to leave the EU by 2018.
He said: “Brexit poses a threat to meeting this target - the risk is difficult to quantify at present because the implications for departure at mid point of the programmes are still unclear.”
He went on: “On the one hand, the UK’s partnership agreement with the European Commission and the funding between 2014 and 2020 may be viewed as a contractual obligation to maintain current programmes for the full period or at least to the conclusion of the exit period.”
If there was to be any extension granted, it would have to be agreed by every EU member state.
Cllr Dance warned: “On the other hand, the UK’s financial commitment to the programmes could cease before then or a moratorium might be imposed on any new bids.”
Labour spokesman Cllr Roger Truelove said the uncertainty highlighted the risk of leaving the EU.
"We heard quite a lot during the referendum campaign about how the UK's contribution might be recycled back into our economy.
"There was the promise to pay it all into the NHS. Farmers who voted Brexit apparently think they are going to receive the same subsidies from our Government.
"I only hope there will be some funding left to support the local economy and I hope Kent will try to expand its export trade to other parts of the world."