Twenty-five secondaries contacted by The TES, who got results this week, found the proportion of youngsters gaining the expected levels rose five percentage points from 64 to 69 per cent on average.
Eighteen of the schools reported their results going either up or down by at least five percentage points. One recorded a jump from 44 to 65 per cent, and another from 49 to 69 per cent.
But teachers expressed concern over the accuracy of the test marking.
Several teachers have complained to The TES online staffroom that the new test has been kinder to lower-ability pupils, who might have been aiming at level 5, but penalised more academic youngsters.
High marks at key stage three are a mixed blessing for schools, as they will then find it harder to obtain good "value-added" figures at GCSE.
One London school is sending some of its scripts back for remarking because it believes its pupils were graded too leniently.
The TES has seen the work of one pupil from this school, who was awarded level 5 in writing. Experienced English teachers, who are opposed to the tests, were staggered at his mark.
The Shakespeare paper said that Henry V used speeches to encourage his men.
Pupils were then asked to write a speech. The London pupil's piece begins:
"Leson up everyone this is the big day of your life! we have to win this match this is our chance to showing what we can do your mum, dad, your parent... they will all be proud, of yous, you are the futur champion your the futur jeneration."
The pupil got 18 out of 50 for writing, which was comfortably a level 5.
Pupils only need 14 out of 50, or 28 per cent, to reach this level.
Another pupil at the same school was given a level 4 - the expected level for 11-year-olds - for work that was barely legible and virtually incomprehensible.
A specialist school in North Lincolnshire is returning all 250 pupils'
scripts and refusing to release the results to parents. The headteacher said he had four separate complaints over the papers. There had been simple addition errors: one paper had 19 plus 19 added up as 28. Two markers, invited in by the school unofficially to look at the scripts, identified serious problems.
The head of the school, where results fell four percentage points this year, said: "English has been a debacle. Trying to sustain teachers' morale and faith in what is supposed to be a nationally-accredited test is almost impossible."
As The TES reported last month, many English markers have reported concerns with a new mark scheme, launched this year, in which examiners mark papers before seeing how many marks a pupil needs to get a particular level.
Nationally, the Government has set a target to increase the proportion of pupils gaining level 5 from 67 per cent last year to 75 per cent next year.
Several schools said their achievements were partly due to teaching improvements under the key stage 3 strategy. Contributors to the TES website complained that results were "bunching" - more lower-ability pupils might gain level 5, but bright pupils were finding it hard to reach level 7.
Doubts have already been raised about this year's KS3 results after the mark pupils needed to gain a level 5 in English was cut from 35 to 30 out of 100.
A Qualifications and Curriculum Authority spokeswoman said: "We are confident that the quality of the marking of the tests is robust. Standards are rigorously maintained every year."
Additional reporting Athalie Matthews and Emily Clark