General secretary Rodney Bickerstaff will issue a petition to the European parliament on 23 November on behalf of those members who will lose out.
And the union will be taking action against the government on behalf of individuals who are disadvantaged by the failure to implement the directive.
UNISON local branches have been asked to identify areas where the directive will have an impact - for example, night workers, shift workers, part time workers or those with no entitlement to annual leave and long hours workers.
Mr Bickerstaff said:
'This directive gives Britain an opportunity to move into the 21st century with out workers being treated decently and equally with other European workers. It's a disgrace that Britons work the longest hours in Europe often linked to low levels of basic pay.
'We want to see the directive implemented properly. The government should be in no doubt that we will challenge them through the courts. We have done this before and will not hesitate to do it again. Workers shouldn't be expected to damage their health through excessive working hours with inadequate rest and holiday breaks.
'More than one million people in Britain are holding down two or three jobs in a desperate attempt to make ends meet. Others are working more than 48 hours a week because of staff cuts or cuts in services which have resulted in staff cuts.
'We need properly funded public services with adequate staffing levels and we need a minimum wage to complement the working time directive'.
In guidelines issued to UNISON branches today, the union stresses the benefits of the working time directive in protecting the health and safety of employees and details what is up for negotiation with employers.
The directive, says UNISON, will be useful in trade union negotiations because it clearly establishes that rest breaks, time off work, annual leave and a limit to the number of hours worked in a week are required for health and safety reasons. It allows working time to be regulated through collective bargaining between employers and trade unions. And it encourages negotiated flexibility and trade union recognition as non-union firms will be dependent on laws or regulations.
Employers in those areas where derogations apply, will have to collectively bargain with unions so that workers receive equal treatment. For example in the emergency services, compensatory time off or a rest break in line with the directive will be negotiated so that staff get their entitlement without affecting front-line provision.
Basic provisions are:
-- rest breaks where working day is longer than six hours
-- rest breaks of 11 consecutive hours in each 24 hours
-- 24 hours rest in each seven day period, in addition to 11 hours
-- 48 hours ceiling on average working week over 4-month period
-- 4 weeks' annual leave (three for the first three years)
-- free health assessments for night workers
-- considerable collective bargaining scope
-- powerful clause on 'adapting work to the worker'.