Magpies, like all other species, are protected under the Wildlife & Countryside Act 1981 and the Wildlife (Northern Ireland) Order 1985. This makes it illegal to intentionally or, in Scotland, recklessly take, injure or kill a magpie, or to take, damage or destroy an active nest or its contents. In Northern Ireland, it is illegal to disturb birds at an active nest.
However, the law recognises that in some circumstances control may be necessary. Killing can only be done if specific conditions are met, and only where non-lethal methods of control are ineffective or impractical.
The UK Governments issue annually general licences (for which it is not necessary to apply individually) under the Wildlife and Countryside Act and the Wildlife Order, some of which allow magpies to be killed or taken by 'authorised persons', using permitted methods, for the purposes of:
preventing serious damage to agricultural crops or livestock
preserving public health
conserving wild birds
preserving air safety.
An 'authorised person' is a landowner or occupier, or someone acting with the landowner's or occupier's permission.
Since general licences are reviewed annually and can be withdrawn or altered at any time, it is recommended that anyone wanting to exercise the licence should first check details on the relevant government department website or contact them for up to date legal advice and the exact terms of the licence.
(http://www.rspb.org.uk/wildlife/birdguide/na
me/m/magpie/legal_status.aspx)