Fast-moving lessons left some students struggling to keep up. Nearly half of the teachers surveyed also believed the stress on pace led to "superficial" learning.
The Strategy or Strait-jacket? report was commissioned by the Association of Teachers and Lecturers. Researchers from King's College, London, questioned more than 100 English and maths teachers in the 205 schools which piloted the strategy.
Catch-up classes for 12-year-olds who failed to achieve the expected level in their last year of primary came in for most criticism.
One teacher said: "I think it is naive to believe children who are behind need more teaching of the same concepts. Children with special educational needs need a totally different approach and content - not more of the same."
Thousands of pupils in their first year of secondary school who failed to reach level 4 at 11, sat progress tests last May . The Government has yet to publish the results.
In 2001 the tests were a flop - with most pupils failing to get over the level 4 hurdle second time around. The two-year ATL study found that English teachers thought the three-part lessons were useful. However, the majority of teachers had serious concerns about the shift of emphasis from works of literature to studying the use of language.
A Year 7 teacher said: "I can't go on reading Treasure Island with my class for more than 20 minutes, because if I don't do something else, I'm not fulfilling my obligation."
In maths, children were doing more mental arithmetic and teachers said there was more interactive teaching. However, some staff perceived a widening gap between the highest and lowest achievers.
Sheila Dainton, ATL education policy adviser, said: "Pupils are getting the message that if they don't at first succeed, they will fail, fail and fail again. There are many positive aspects to the strategy, but the strategy is failing the very children it was designed to support."
Difficulties in recruiting and retaining staff was reported as a major obstacle to implementing the KS3 frameworks successfully.
A government spokeswoman said: "The ATL survey is based on the pilot. We have already strengthened our support programmes with improved catch up and booster material."
To order a copy of the report, priced pound;8.99, call 0845 4500 009 or go to www.askatl.org.uk