Some of those falling behind are described as "invisible children" who avoid drawing attention to themselves.
Education officials are not "banning" the practice, but say some respond better when taught in smaller groups.
A Department for Education and Skills (DfES) spokesman said: "We would categorically never prescribe what teachers do in their own classrooms like this.
"The report is based on what teachers and schools tell us and has been welcomed by them."
"Invisible children", the report finds, are quiet and undemanding and do not mind if they receive attention or not.
The research suggests helping these pupils by avoiding asking for children to put their hands up, instead choosing who should answer.
These pupils, the report adds, would also benefit from having 30 seconds to consider their answer.
