The UK has received just over a third of the money it had hoped to get as reimbursement for the billions lost through the foot and mouth crisis.
More than six million animals were slaughtered during the outbreak
Ministers had hoped to get £900m from the European Union Vet Fund to help with animal slaughter and other costs.
The department for the environment, food and rural affairs (Defra) confirmed it had been granted £349m.
Defra said the cost to taxpayers would have been higher if it had not achieved "rapid eradication" of the disease.
But ministers were criticised after the crisis for failing to prepare properly for an outbreak on that scale and for not halting the spread of the disease quickly enough.
It is estimated the whole crisis cost the country up to £8bn.
More than £1.3bn has been given out to farmers as compensation for the loss of their livestock.
In September this year a former Defra vet said the culling of thousands of animals during the 2001 outbreak was unnecessary.
Dr Nick Honbold said the study of field data taken from Defra's databases and records found no evidence the contiguous cull helped to hasten the end of the outbreak.
As part of the cull, healthy animals on farms next to infected ones were killed, despite protests from farmers and vets.
Official figures from Defra show that 6.5 million animals were slaughtered.
The UK had claimed £1.6bn from EU fund for animal disease epidemics, but under the rules only 60% of a claim can be reimbursed, said Defra.
Officials said the settlement was much higher than the 23% originally proposed by the European Commission, and was higher in percentage terms than other countries had received.
The UK has already been handed £280 million, while the rest is due to be paid on by 31 December.
"The UK had to act swiftly and on an unprecedented scale," added Defra.
"As such financial resources were severely stretched. There has been a full review of our contingency plans and state of preparedness for the future in light of the lessons learned from 2001."