They have been told by the Intervention Board that they have until 31 July to use export licences issued before the ban: failure to do will result in a fine.
One exporter, First City Trading, faces a bill of pounds 34,602 if it does not use its licences for the export of 92 tonnes of beef. Its managing director, Martin Richardson, said: ''It is ridiculous. We are being penalised for not using our our export licences at a time when we cannot export beef. The Intervention Board should take a stand on this.''
When exporters apply for a licence, they have to put up securities of between pounds 240 and pounds 400 a ton of beef.
Once the declared amount of beef has been successfully exported, the traders may claim a refund from the European Union.
''Since the ban, there has been an increase of 9 per cent on the refunds, so we are stuck with low refund licences that no one wants to buy,'' said Mr Richardson, who used to export 800 tons of beef a month before the ban brought trade to a halt.
"We have been pressing the Intervention Board to cancel the licences and release our securities. It seems reasonable under these circumstances, but they have so far failed to do that," he said.
He stressed that exporters also faced a loss on refunds they used to receive once beef had been exported.
To maintain European farmers, exports to countries outside the EU where prices are much higher are subsidised.
Because beef that had been exported before the ban was imposed had not been through customs, or was on the high seas at the time, the exporters are not entitled to those refunds. Mr Richardson said he stood to lose about pounds 760,000.
A spokesman for the Ministry of Agriculture, Fisheries and Food called for dialogue to resolve the issue. "These are exceptional times. If they are facing difficulties they should speak to us," he said.