Less than four out of 10 pupils in England's state and private schools achieved C or better in all three subjects, according to the Department for Education and Skills.
The statistics also revealed that the proportion of pupils gaining five Cs or better in all subjects rose to a record 52.6 per cent. This figure includes pupils educated in private schools. The increase, officially put at 1 per cent, was lower than the Government's target of 2 per cent.
Ministers also face a struggle to hit two other key targets next year.
Overall, 38 per cent of pupils achieved Cs or better in English, maths and science, down from 39 per cent last year. The proportion getting a C or better in maths fell from 49 per cent to 48, while the figure for English alone climbed from 55 to 56 per cent.
Those statistics are bad news for a Government which has staked its reputation on improving grades in the compulsory subjects.
Ivan Lewis, junior education minister, said he was particularly concerned about maths but the Government would await the results of its inquiry into the subject, which reports this month, before deciding how to address the problem.
But Mr Lewis said the figures overall were "going in the right direction".
This year's candidates had not benefited from initiatives launched since 2001, including the key stage 3 strategy and a new focus on behaviour and attendance, which he hoped would improve results.
He highlighted statistics showing that schools in deprived areas were closing the gap slightly on the rest (see box). Mr Lewis said: "For the second year running, the poorest schools have improved significantly faster than the rest."
However, the proportion of pupils achieving five or more passes (A* to G), including English and maths, fell from 87.1 per cent last year to 86.3 per cent. The DFES 2004 target is 92 per cent.
Ministers have also pledged that every local authority will see at least 38 per cent of pupils getting five Cs or better by next year. This year, 12 failed to hit this target, compared to 18 last year.
The gap between boys and girls closed slightly this year, with 47.5 per cent of boys getting five Cs or better, against girls' 57.8 per cent.
Teachers' unions welcomed the rise in the five A*-to-C rate as evidence of improving standards.
Assessment: how to make it a force for good 16-page magazine this week GCSE facts
* Percentage of pupils getting five Cs or better up from 51.6 in 2002 to 52.6 in 2003
* Percentage getting five Gs or better down from 87.1 to 86.3
* Proportion getting Cs or better in all of English, maths and science down from 39 to 38 per cent
* 57.8 per cent of girls got five A*-to-C grades, compared to 47.5 per cent of boys
* 5.4 per cent of pupils did not get any GCSEs
* The five A*-to-C score for schools in challenging circumstances increased from 26.5 to 28.5 per cent
* Number of local authorities with less than 38 per cent of pupils getting five A* to Cs down from 18 to 12