The failure rate doubled in maths, despite an upward trend in other subjects, and Professor David Burghes from Exeter University blames the Government's curriculum quango, the Qualifications and Curriculum Authority.
He says that the QCA imposed a "bizarre" restriction which makes it harder to pass two of the three maths papers available.
This year, for the first time, D grade candidates failed if they attempted the most difficult, "higher tier" exam. Lowest pass or F grade candidates failed if they took a gamble on the "intermediate tier". Last year, they would have passed.
The Secondary Heads Assocation has also voiced its concern. Its new general secretary, John Dunford, has written to the QCA to complain.
Mr Dunford said: "It's something people didn't pick up in August. The tiering rules have caused large numbers of students who might have got a moderate grade to get no grade at all. It's crazy."
The pressure to enter candidates for the top tier (grades A*-C) has increased because it is the only one that registers in the national league table of results.
The QCA has launched an investigation into the changes, which were intended to produce a clear distinction between the three different levels of maths exam on offer. But it denies that the new "tiering" system accounts for the high failure rate.
Last summer saw an enormous rise in the number of failures in maths, with 35,000 students receiving no award. The percentage of failures more than doubled from 2.1 to 5.2 per cent.
Professor Burghes points out that the numbers getting unclassified marks increased by 3.1 percentage points. At the same time, the total getting the lowest pass grade Fs declined by 3 points.
"This would appear to be accounted for by candidates falling off the edge. That is, they were entered for the intermediate tier but failed to achieve a grade E. So they were awarded a grade U."
Professor Burghes said: "Most of these students can try again, but for many of them it is a real disaster. Indeed the word scandal comes to mind."
At the time, a number of theories were advanced for the decline, including the national shortage of skilled mathematics teachers.