If someone is angry about waiting for treatment in a hospital accident and emergency department and they swear and threaten a receptionist, or if a drunken patient swings a punch at a nurse, the police would usually be called.

Few would argue with that, and many hospitals have a "zero tolerance" policy about violence as a result.

But the issue is more complicated if a patient is on a mental health ward, and the violent behaviour could well be a consequence of their medical condition. "Nobody should have to come to work expecting to be assaulted – that shouldn't happen," says Donald Lyons, chief executive of the Mental Welfare Commission (MWC).

"GPs surgeries, and A&E departments and other NHS settings often have clear signs posted warning that aggressive behaviour and violence towards staff will not be tolerated. That is absolutely correct; but it is a different situation where you are dealing with someone who has a mental illness, where their behaviour is driven by psychiatric symptoms – hearing voices, perhaps, or a maybe a learning disability."

The idea of zero tolerance in that context is more complicated, and that is why the MWC has just issued new guidance, aiming at helping hospitals and other care settings chart their way through a potentially explosive area.

The guidance says zero tolerance runs the risk of "misinterpretation" in this context. It clarifies that a workplace can aim for zero tolerance of staff or other patients feeling at risk, without that necessarily meaning a rigid attitude to the patients responsible.

"We've investigated the case of a woman who was summarily discharged from hospital because of violent behaviour, when it was really quite clear that her episodes of agitation and aggression towards property were as a result of her being mentally unwell," Mr Lyons explains. "We felt sometimes staff were very hasty to take action against people with a mental health problem, when that behaviour was really a consequence of their illness.

"We were concerned that sometimes every assault, no matter how minor, was being reported to the police, and police were getting involved solely to punish behaviour that staff deemed unacceptable. We felt people could do with more direction, to get away from this idea of punishing the individual."

The guidance has been drawn up following an intensive session to which relevant parties, including mental health workers, patients, charities, carers, police and human resources managers, were invited. A number of controversial cases which had come to MWCs attention were then considered, with the experts not allowed to leave until they had answers. "We asked them what should happen in these various situations and didn't let them out until we'd got the guidance," Mr Lyons explains. "It is surprising how much consensus they develop."

It's a pragmatic approach which the regulator has used on a number of occasions now to deal with controversial areas from the covert use of medication to the rights of people with mental health problems to have a sexual relationship.

The guidelines which have emerged emphasise the need for proper planning to ensure the safety of everyone involved is paramount. While the clear suggestion is that involving the police isn't always helpful, it is made clear that any victim of an assault will always have the right to report that. However Mr Lyons says prevention will always be better than cure. He emphasises that it is only a minority of people with learning disabilities or mental health problems who will pose a risk of violent or aggressive behaviour. But one of the biggest concerns in patient psychiatric care is that patients often feel unsafe. "It is not necessarily that the number of incidents is high, it is that service users feel unsafe. Everybody involved must feel safe and get support." Mr Lyons says.

We know certain factors can improve this, Mr Lyons adds. The ethos of a health care setting, the amount of space within it and what there is for patients to do to occupy themselves all matter, as do good policies.

These might still include involving the law, he says, but it should be done sensibly. In one case a young man with a psychiatric illness was thought to be behaving aggressively in order to get prescription pain killers which he could misuse or sell on the black market. The decision was taken that if he did it again the police would be called immediately.

"They took that decision, but didn't tell the patient, his carers or relatives. If you are going to do something you have got to do it well. One of the lessons here is communication, communication, communication," Mr Lyons adds.

Another issue is that where a decision is taken to remove a patient – for example to a police station – ongoing medical care must be managed. "There cannot be a sense that medical staff say: 'Phew, thank goodness for that,' and leave it. The hospital must make sure there is ongoing care and treatment and continuity with things like medication. It is not down to police."

The guidance has been welcomed by Scotland's leading mental health charity.

Carolyn Roberts, head of Policy and Campaigns at SAMH (Scottish Association For Mental Health), said: "People who are receiving care and treatment for a mental health problem have a right to expect that they will be in a safe environment. So we welcome this new guidance from the MWC. It's good to see such a strong focus on preventing incidents and a recognition of the fact that very few people with a mental health problem are ever violent. We think this is a proportionate and sensible response."