Gill Morgan revealed on the first day of the confederation's annual conference that the behaviour of some professionals in the past year had left her 'ashamed'.
Unison and the British Medical Association were singled out as she criticised the growing tendency for organisations to launch personal attacks on other groups and individuals.
'I was taught that the stages of medical debate were statement, counter-statement followed by personal abuse. We now seem to have a new model which misses out the first two stages,' she said.
She went on to express her regret at last month's departure of BMA chair James Johnson following a row over junior doctors' recruitment.
Reconfiguration rows and criticism of targets had also undermined the work that NHS staff do, she said.
She called for a 'moratorium on hyperbole' to ensure public squabbles did not detract from patient care.
Dr Morgan also told delegates that trust boards need to be given more autonomy, with non-executive directors given a greater scrutiny role.
She accepted this would place 'an enormous burden' on strategic health authorities, which must 'manage increasing diversity rather than the conformity and linear expectations of the past'.
She added: 'They must judge performance in a much more nuanced way to allow local areas to develop a flavour of their own and they must stimulate change in a way that supports innovation.'
Less bureaucracy would ease the burden on managers and enable them to focus on patient outcomes, she said. 'It's ironic that we take so much criticism as managers for being pen-pushing bureaucrats, when it's bureaucracy that frustrates us the most,' she said.