A strong science department in an otherwise average school would be able to advertise its strength under the scheme which is mooted by councils involved in the Labour's pound;350 million Excellence in Cities initiative.
The awards will not be part of the official British Standards Institution's Kitemark scheme.
In a letter to local authorities, Michael Barber, head of the Department for Education and Employment's standards and effectiveness unit, said: "We would be interested to see local proposals for kitemarking departments in addition to beacon schools."
He added: "One possibility may be to network beacon schools with effective departments and so create a stronger partnership."
The scheme, which would be administered by local councils, has been called potentially divisive by teachers' leaders.
John Bangs, assistant secretary of the National Union of Teachers, said: "The teacher awards showed there was a lot of good practice in schools. It would be better for LEAs to encourage all schools with good ideas to share them on a website, rather than have a formal, and bureaucratic kitemark system."
Kitemarks are awarded by the British Standards Institution for products. The ISO 9000 certificate is awarded to organisations such as schools.