A three-member bench ruled that only the National Public Service Commission (NPSC) can issue orders to the Provincial Council Chief Secretary, an officer under the NPSC.
The court's verdict came on a rights petition filed by Chief Secretary Vijayalakshmi Ramesh challenging a circular issued by the chief minister.
Ramesh had alleged in her petition that Wigneswaran was acting in interference with her employment in his bid to remove her from the office.
Through his directive titled Administrative Standing Instructions, Wigneswaran wanted the Northern Provincial Council's chief secretary, secretaries and head of departments hence forth liaise via the elected board of ministers, rather than directly with the Governor.
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Wigneswaran, of the main Tamil party the Tamil National Alliance (TNA), won the first-ever Northern Provincial Council election last September.
He has been demanding the removal of Governor GA Chandrasiri, who was re-elected in May despite opposition from the TNA.
The Tamil party has been complaining of interferences by the governor in the functioning of the council.