GCSE grades in science and maths have fallen in Wales following a change in the way the tests are set and marked.
Across all subjects, overall pass rates in Wales remained stable at 98.7% while the gap in top grade pass rates between Wales and other UK nations narrowed.
Examination boards have also linked a fall in maths, science and English pass rates to an increase in pupils taking those exams a year early.
The education minister said "despite rigorous tests" students had done well.
Huw Lewis said: "Our work to build on the rigour of qualifications remains a key element of our agenda to raise standards in Welsh education.
"Despite rigorous tests our students' performance in GCSEs shows that the overall pass rate remains stable at a high 98.7%, with passes at A*-C at 65.7% which is encouraging."
Equivalent figures for A* to C passes were 67.9% in England, 76.5% in Northern Ireland, and 68.1% across the three nations.
The proportion getting an A* or an A fell from 22.4% to 21.3% across the three nations while in Wales they remained the same at 19.2%.
Sciences saw the biggest drop in Wales following the new test arrangements - pass rates at grade C or above fell from 57.3% in 2012 to 51.2% in 2013, with a similar fall across the three nations.
In maths, 52.8% of Welsh candidates achieved a grade C or above compared with 55.5% in 2012.
BBC Wales education correspondent Arwyn Jones said that there was an ongoing drive to make core subjects increasingly difficult, not just in Wales, but in England and Northern Ireland too.
Last year's results were overshadowed by a re-grading row over English exams.
The then-Education Minister Leighton Andrews came under fire when he ordered the WJEC board, which sets most of the GCSEs taken by Welsh pupils, to re-grade English language exams after the results were published.
He said grade boundaries were set in a way that was unfair to candidates in Wales and they had been the victims of an "injustice".
Nearly 2,400 pupils in Wales received better results after the review, resulting in a row with the UK government and a break with England.
This year pupils in Wales sat a totally different paper to those in England, also marked in a slightly different way.
An extra 5,455 pupils sat the English exam in Wales this year - up 15.4% - with a fall in pass rates at Grade C or above from 60.9% last year to 59.6%.
The Joint Council for Qualifications - representing exam boards across the UK - said the decline in pass rates for English was explained mainly by an increase in the number of entries by 15-year-old pupils, whose results were significantly poorer than those of 16-year-olds.
The council said it was also a factor in falling grades for maths and sciences along with the changes in tests.
However, WJEC defended the practice of letting pupils take GCSEs early.
"The main consideration should be that young people take GCSE assessments at the right time in the learning programme being provided for them, and that they are given the opportunity to achieve their very best," said a spokesperson.
"In some circumstances, taking a GCSE earlier than the summer of Year 11 can be appropriate, e.g. when Mathematics is taken early to allow Additional Mathematics to be taken in the summer of Year 11."
'Level playing field'
But the Welsh Conservatives' shadow education minister Angela Burns said she was worried about pupils taking GCSEs early.
"The rise in GCSE entries for 15 year olds seems very unfair because it removes the level playing field and could be setting some pupils up to fail," she said.
"GCSEs are a challenging course and should take the full two years to allow young people to learn and fully develop their skills before being assessed."
Mrs Burns said she was also concerned about the performance of boys.
"These results show a persistent gender gap, growing to nearly 10% for A* to C passes, which risks leaving young men as the most disadvantaged and under-skilled group in the employment market," she said.
"What is particularly worrying is that this week's reading and numeracy test results for 7 to 14 year olds showed similar gender gaps, which bodes ill for these year groups taking their GCSEs in the next decade."
Meanwhile WJEC said there had been record entries and achievements in the Intermediate and Foundation levels of the Welsh Baccalaureate.
Intermediate entries rose by more than a third to just under 14,000 as the exams were rolled out to more schools, with the pass rate for Intermediate diplomas up from 73% in 2012 to 79%.
Foundation stage entries rose more than 10% to nearly 3,000 with pass rates rising to 77% for the diploma and 83% for the certificate.