Teaching underachieving black boys in separate classes for some subjects has been rejected by the government.
Black boys' exam results are below average
Trevor Phillips, head of the Commission for Racial Equality, suggested they might benefit from such a move, which had been tested in the United States.
But the Department for Education and Skills said such separation would have "negative effects" and risked "stigmatising" black pupils.
Head teachers had questioned the legality of racially-divided lessons.
In England, only 27% of Black Caribbean boys got five or more good GCSEs last year, considerably below the national average for boys of 46.8%.
Among girls, 44% of Black Caribbean girls achieved five or more good GCSEs, against a national average for girls of 57%. Black Caribbean pupils are also three times more likely than white pupils to be excluded.
'Wall of attitude'
After visiting a scheme in the US, Mr Phillips suggested some black boys were hampered by a lack of self-esteem and positive role models, as well as an attitude that being clever was not cool.
"If the only way to break through the wall of attitude that surrounds black boys is to teach them separately in some classes, then we should be ready for that," he said.
But the Department for Education and Skills said research showed segregation was not the best way forward and could "have negative effects in terms of teacher and pupil expectations".
"There are schools where black boys are achieving at the highest level. These schools don't segregate pupils in the way suggested," said a spokesperson.
The Secondary Heads Association warned any segregation based on skin colour could create "great difficulty" and may be illegal.
SHA deputy general secretary Martin Ward told BBC News: "Saying to a pupil 'right, I want you to go to room five instead of room one because you need extra help', that's one thing.
"Saying 'I want you to go to room five instead of room one because you're black' potentially could create a great deal of difficulty."
But Shahid Malik, chairman of the Labour Party's ethnic minority forum and a former CRE commissioner, said "many African-Caribbean people would feel it was a debate whose time had come".
Speaking on BBC's Inside Out programme Mr Phillips had also suggested black fathers not living with their sons should be denied access to them if they refused to attend parents' evenings.
And he called for more male black teachers, tempting them with extra cash if necessary.
His comments were not aimed at black girls - GCSE results in England show that "black African" girls are scoring higher grades than "white British" boys.
The CRE said that Mr Phillips had not called for all black boys to be segregated in schools.
It said he was "not sure" how the US measures would work in the UK, but that he felt "we should look at the scheme to see if we can learn anything from it".
Inside Out will be broadcast at 1930 GMT on Monday on BBC One in the London area.