Farmers desperately waiting for subsidies were told yesterday they will receive a share of the cash after the Government admitted not all payments would be made by the end of June.
Environment Secretary Margaret Beckett said "substantial partial payments" of the Single Farm Payments will now be made after the Rural Payments Agency's acting chief executive Mark Addison said he was not confident all the payments would be made on time.
In a written Ministerial statement, Mrs Beckett said she had authorised work on a system to make the partial payments.
She added that it "should be deployed as soon as it is operationally possible to do so".
Mrs Beckett said: "The acting chief executive has, however, now told me he does not feel confident that he can say with complete assurance that the RPA will be able to make all of the full payments by the end of June.
"Given that advice, I have authorised that work on a system to make substantial partial payments to the remaining claimants should now be given priority and I further decided that the system should be deployed as soon as it is operationally possible to do so.
"The RPA will, in the meantime, continue to make full payments when claims have been fully validated, with historic claimants having priority."
Mrs Beckett added that so far £362 million had been paid out, which represented "useful progress", she claimed.
Last month Mrs Beckett announced "urgent action" over the administration of the scheme, replacing chief executive Johnston McNeill. She added that there were "structural issues in the RPA.
The National Audit Office has said it is investigating the Government's failure to pay farmers on time, which has left hundreds struggling to pay bank loans and settle bills.
A spokesman on behalf of the National Farmers' Union, Country Land and Business Association and Tenant Farmers' Association, said: " The organisations are encouraged that the Government has listened to the industry's concerns and has responded positively to their requests.
"While this is good news, the organisations strongly expressed their anxieties about the problems of 2006 applications and again urged that every opportunity is taken to introduce greater flexibility into the system."