Confident reading and writing is crucial to children's secondary school development, a study suggests.
The pupils preferred to be in groups but were likely to work alone
Interviews with pupils failing to make progress in 46 schools in England found they tended not to see themselves as readers, even if they did read at home.
They struggled to express their ideas in science, and did not see connections between different aspects of maths.
Government standards advisers also spoke to their teachers and suggest strategies schools might use to help.
The report, focusing on the core subjects in Key Stage 3 (ages 12 to 14) is the third in a series.
Young People's Minister Kevin Brennan said the report's findings should not be taken as an indication of the likely outcome of this year's national curriculum tests.
The results of those are due to be published on Tuesday.
The concern centres on children who were doing well - they reached the expected level (Level 4) at the end of their primary schooling.
But their rate of progress then slowed or even stopped and they were at risk of not making Level 5 at the end of their third year in secondary school.
"In English, pupils who were making slow progress did not see themselves as readers, though many of them said they had enjoyed particular books or authors," the report said.
"They saw the magazines, newspapers, non-fiction or 'lightweight' fiction that they often read at home as different from the texts they read in class."
In science, "many found it hard to commit their ideas to paper".
"Some found words such as 'chromatography' and 'distillation' difficult to use, and found questions harder to answer if there was a long preamble."
In maths, "these pupils rarely saw relationships and connections, such as between fractions, decimals and percentages".
The report said it did not wish to stereotype the pupils but in general they were often quiet, embarrassed about making mistakes and unwilling to ask for help.
They wanted to work in groups but were mostly on their own, and often gave up easily.
"They relished praise and reassurance."
Mr Brennan said: "Amongst other conclusions, this report brings out the links between reading for pleasure and academic performance.
"It highlights the fact that boys tend to make slower progress, and read less, than girls. That is why we are funding every secondary school library to acquire new books targeted at teenage boys, exactly the age group covered in this report."
He added: "We want to help teachers to push every pupil in their class to achieve as much as they can.
"These practical reports home in on the specific barriers that prevent children from doing that - group by group and subject by subject."
National strategies could be adjusted accordingly and at school level teachers could intervene early to address any problems and be confident they were giving the right extra support.
So-called progression pilots are due to start in 484 schools from September.