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The ferry firm infamously offered millions from central government to dock in Ramsgate despite having no ships has gone bust.
Seaborne Freight has entered voluntary liquidation while still owing £2 million to tax collectors and in loans, according to the Companies House government website.
The firm owes £1.2m to trade and expense creditors, £723,000 in directors and other loans and a £100 HMRC corporation tax bill.
However, Seaborne has only £39,120 in assets to liquidate from furniture, computer equipment and cash in the bank.
The firm was given a £13.8m contract from then-Transport Secretary Chris Grayling to ship food and medicine between Ramsgate and Ostend in Belgium. This was meant to relieve Dover's port in case there was a no-deal Brexit.
The former Transport Secretary was forced to cancel the contract only a month before the original Brexit deadline of March 29 last year - because the firm was revealed to have no ships.
Councillors in Thanet also criticised the plans for not taking into account the cost and infrastructure needed to carry out the plans.
Grayling lost his position after Boris Johnson's election in 2019. At the time, The Department for Transport said no taxpayers' money was ever given to Seaborne.
However, Thanet councillor Karen Constantine (Lab) says the waste of councillors' time considering the issue does cost taxpayers money.
She added: "I'm very sorry Seaborne are going into liquidation - but it's not a huge surprise.
"There was a plan for Ramsgate Port that was never predicated on any factual information whatsoever. It was a complete flight of fantasy and governement ministers involved, Chris Grayling most of all, were incompetent and bumbling.
"They weren't acquainted with the port, did not understand its limitations and were not at all focused on what the people of Thanet actually need. They really need a proper plan for jobs, especially with youth unemployment rising to 20%."
With the threat of a two-day backlog at the Port of Dover and the expanded building of lorry parks, the councillor worries about "real strife in East Kent" after the Brexit deadline.
Cllr Constantine added: "There is currently a consultation being done about what the future of the port might look like.
"I think there needs to be a full consultation with the people of Thanet to come up with a plan for the port which is realistic. But ultimately one that will create jobs and can help our tourism industry - which has been growing."