The proportion of U-grades doubled this year, and the new "tiering" system was blamed. The tiered papers - graded by difficulty - offer a limited range of grades and could penalise pupils entered for the wrong one.
But the Qualifications and Curriculum Authority rejects this explanation.
It says that this year, for the first time, results included candidates who did not complete the entire exam - and most failed as a consequence. Previously they were excluded from the statistics. The failure rate in maths rose from 2.1 to 5.2 per cent.
As Professor David Burghes from Exeter University has pointed out, a large proportion of pupils appeared to fail the middle-ranking tier - possibly because they were hoping for a C grade (not available in the bottom tier).
The QCA is investigating. It must still explain why the number of incomplete exams seems higher in maths than other subjects.