Pupils should have a say on punishments for bullying, new guidelines will say.
Victims may get access to break time safe rooms but those who retaliate against bullies can still be excluded, the government guidance will add.
It comes after an education select committee report, published in March, said that the circumstances should be taken into account in such cases.
The guidance for England's schools will not treat different types of bullying separately to avoid creating "ghettos".
Bullies must learn from their punishments, ministers say
However, the government says faith schools - which have been accused of ignoring homophobic bullying - must not just sign the Anti-Bullying Charter and then ignore it.
The committee's report was wide-ranging and the response follows suit.
Although it has just been published, it was sent to the MPs for consideration a month ago, referring repeatedly to plans to issue a "suite of guidance".
Unusually, Education Secretary Alan Johnson has since written to the committee to say: "We have reconsidered our approach" - partly because of talks with the education unions.
Comprehensive guidance would "ensure that approaches to bullying are not fragmented, that no 'hierarchy' seems to exist, and that certain types of bullying do not become ghettoised", he said.
But the National Autistic Society has complained that guidance on bullying related to disabilities is to come later.
"It seems that the government has yet again failed to place the same importance on eliminating disablist bullying, as it does on other kinds of prejudiced-based bullying," said spokesman Benet Middleton.
The Department for Education and Skills agrees with the MPs that pupils should be consulted about the sanctions for bullying.
"This will ensure pupils view sanctions as fair and will make them feel they have an influence over tackling the issue."
And it agrees schools should target their attention on the times and places where bullying is most prevalent.
It says schools should look at patterns of staff supervision and investigate having "quiet play" areas in playgrounds or "short-term safe rooms for use at break times".
The department says: "Pupils should not be excluded for being bullied, even if the school believes they are doing so for the child's benefit."
But it adds: "Where a pupil has been bullied and is provoked into 'hitting out', they might be excluded from school for violent behaviour."
This was "for the head teacher's judgement".
The unions were unhappy at the MPs' proposal that there should be an independent appeals procedure for bullying victims unhappy with schools' responses.
The government says ministers are awaiting a final report from the Office of the Children's Commissioner before making any decisions.
But ministers do not agree with the committee's call for more reliable data.
Schools will be encouraged to be open in reporting incidents but there would be "logistical difficulties" in making this statutory.
MPs had said the extent of bullying was unclear
Chris Cloke of the Anti-Bullying Alliance said this was disappointing.
"Whilst it would undoubtedly be difficult to develop an effective way of collecting such data, this is not enough of a reason not to do it."
Some local authorities were already doing so.
"Without this kind of data we must guess what the live issues are, and are in danger of doing what seems easy, trendy or important from an adult viewpoint."
The government has commissioned the alliance to carry out more research into tackling bullying.
The research team has concerns about the plethora of anti-bullying techniques and the increasing "marketability and commercialisation" of some of them and will try to determine what works best.