The Directive provides that no person should work more than 48 hours a week averaged over four months, and allows for regular breaks and paid holidays.
'We believe the Directive will have a significant effect on local government workers,' a spokesman for the Local Government Management Board said this week.
Unison general secretary Rodney Bickerstaffe said public sector staff are working more than 48 hours a week because of staff cuts or cuts in services.
The Directive exempts senior managers with autonomous decision-making powers, but Unison believes all officers at deputy chief officer level and below are covered.
'We want to see the Directive implemented properly. The government should be in no doubt that we will challenge it through the courts,' Mr Bickerstaffe said.
Local Unison branches have been asked to identify areas the Directive will affect.
'We're trying to gather an array of cases, [including] senior managers who are working unofficial overtime to meet the demands of the job,' said Liz Snape, Unison policy and research officer.
From 23 November, when the Directive comes into force, Unison will begin negotiating working hours policies with employers.
The Directive provides for staff to opt voluntarily for longer hours. But employers have to agree this with the individual, state their reason for wanting the person to work extra hours, and keep a record of the hours worked.
The government mounted a legal challenge to the Directive in 1993, which was overruled by the European Court of Justice on Tuesday. Whether or not the government withdraws threats made this week to block the Directive, the Trades Union Congress argues that it automatically applies to all public sector workers.