Peter Wanless, director of the families group at the Department for Children, Families and Schools, said: "There's a really big issue around white boys eligible for free school meals that we are going to have to address as a country. Ministers are aware of this."
Speaking at a conference on tackling low achievement, Mr Wanless presented figures showing only 22 out of 100 white boys eligible for free meals achieved C or better in GCSE English this summer.
Some 42 per cent got no higher than E and 18 per cent were not even entered for the exam. By contrast, national averages showed 59 per cent achieving C or better.
Mr Wanless said some schools were bucking the trend. Robert Clack Comprehensive in Barking and Dagenham, east London, had a strong culture of discipline and good behaviour, a commitment to meeting parents and addressing their concerns and a good local reputation, he told the Children's Services Network conference.
Ministers have introduced new targets aiming at combating low achievement, including narrowing the gap between the performance of pupils on free meals and those not at key stages 2 and 4.
This, he said, was "raising the stakes", putting more pressure on both schools and the Government to perform. The lowest-achieving children could not be ignored.
He said: "The schools system is failing to deliver for these children at the moment. The national Government has put its money into changing the accountability regime so that we will not just be judged on raising achievement but on raising achievement and narrowing the gaps."
Statistics presented by Professor Geeta Kingdon, of London's Institute of Education, showed white pupils eligible for free meals were more likely to do poorly than children from ethnic minorities.
Professor Robert Cassen, of the London School of Economics, said league tables were helping to encourage underperformance by concentrating pupils from poorer backgrounds in certain schools.