About 200,000 secondary school pupils are in the top 5 per cent of the school population, according to the English and maths national tests they sat as 11-year-olds.
But ministers are concerned that no more than half of these pupils are members of the National Academy for Gifted and Talented Youth, which gained its 100,000th member this week.
Lord Adonis, schools minister, wrote to all secondary heads this week, supplying them with access to the list to see whether any of their pupils are eligible for the gifted and talent scheme.
He said: "We must stop the terrible waste of talent when children don't reach their full potential. This register will ensure they are identified early and do not lose out because they come from a deprived background."
He said schools could also identify gifted and talented pupils through other means, such as outstanding pieces of work, teacher assessment and classroom observation.
The register will later be expanded to include all four to 19 year-olds identified as gifted and talented by their schools.
But headteachers remain concerned about the use of test results as a gauge of ability.
John Dunford, Association of School and College Leaders general secretary, said: "Children are under quite enough pressure taking these tests without also wondering whether they will be put on a list of top performers."
He said that although the register was designed to ensure that gifted pupils from poorer families received extra support, it would lead to pressure on heads from middle-class parents to include their children.