Cornwall Council estimates that the county and Isles of Scilly could lose out on the funding which would have benefited local communities.
Julian German, the council's cabinet member for economy and culture, said the county faced a massive black hole following the Brexit vote.
"I estimate that Cornwall and the Isles of Scilly could lose out on £350m of funding that would have helped our residents and local businesses," he warned.
"The limited guarantee for some schemes leaves Cornwall hundreds of millions of pounds short of what we were promised we would receive by MPs who backed the Brexit campaign."
See also: Brexit 'has major rural implications'
Funding streams including contracts for EU structural funds and European Maritime Fisheries projects starting after the Autumn Statement were not guaranteed, said Mr German.
"This simply isn't good enough," he said.
Mr German said Cornwall Council was supporting a Local Government Association campaign for all EU funds to be honoured.
"EU funding, or its replacement, is vital to support economic regeneration, helping individuals to gain new skills and businesses to create well paid jobs."
"Unlike UK funding streams, EU funding has been allocated according to need. This is a really important point for Government to remember
"Cornwall Council will keep advocating for resource which is focussed on closing the economic and skills gap between Cornwall and the rest of the UK.
Mr German said the local authority would continue to work hard with our MPs and partners to try and secure the funding that would otherwise be lost.
He added: "Cornwall Council will also be working closely with government to ensure that as many projects as possible are contracted before the Autumn Statement deadline."