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The company said the job cull was due to growing competition from its rivals and not due to the economic downturn.
GSK currently employs around 18,000 people in the UK in its corporate management, manufacturing and research departments.
The company began restructuring in 2007 in an effort to increase its exposure to developing countries.
A GSK spokesman commented: "We don't announce big headcount reductions until we talk to the unions and work councils first.
"We have a good relationship with the unions and we've had ongoing consultations with then for the past years."
GSK says it is committed to combating the World Health Organisation's three priority diseases: HIV, tuberculosis and malaria.
More than 15,000 people work in the company's research teams.
