Environment Secretary Margaret Beckett has told MPs she recognises there is a "human crisis" caused by delays in subsidy payments to farmers.
Mrs Beckett: Under fire from MPs
Mrs Beckett and minister Lord Bach are facing calls to resign over the delays.
The government initially promised to pay the subsidies by February. Now the Rural Payments Agency cannot be sure they will be paid by the end of June.
Mrs Beckett, who denied payments were late, said "partial payments" of 80% of the amount claimed would now be paid.
For the Tories, shadow agriculture minister James Paice said farmers and their suppliers were facing "huge amounts of debt".
He said Mrs Beckett had needed to take control of the issue from her minister Lord Bach "who had spent months criticising anyone who's forecast this crisis whilst failing to grasp the seriousness of the situation".
Mr Paice said she must have lost confidence in Lord Bach's ability and asked: "How can the industry have any confidence in him?"
Mrs Beckett said she still had confidence in Lord Bach and praised him as an "assiduous and hardworking minister".
"I fully recognise there is a human crisis in the farming community and that is why we're doing everything we can to resolve it," she said.
"There is genuine distress, genuine concern and, in many quarters, anger at these difficulties and real anxiety for many in the farming community."
The new system of payments means farmers receive one annual sum instead of a series of payments.
The new system calculates what subsidy each farm should get according to past receipts and their land area.
Mrs Beckett denied the payments were late as there was a "payment window" that did not close until the end of June.
Liberal Democrat environment spokesman Chris Huhne asked Mrs Beckett to promise that any farmers whose payments are not completed by the end of June will have their interest costs covered.
Mr Huhne called for her to consider her position saying the difference in payments in England from Scotland and Wales showed policy decisions, not just implementation problems, were involved.