No casualties were reported in the blaze, police said.
Security officials said electric short circuit seems to be the likely cause of the blaze as there was a little likelihood of sabotage since the complex was well guarded.
The state government has ordered a probe into the incident and asked the Secretary( General Administration Department) Sheikh Mushtaq Ahmad to submit a report within 15 days. The Civil Secretariat houses all the top government offices of the state including those of the chief minister.
Flames and smoke were seen billowing from the wooden structure adjacent to the main building of the Civil Secretariat, the seat of the state government.
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The fire was brought under control after nearly a two-hour operation by several fire tenders.
The first floor of the building was destroyed in the blaze and the records of key departments reduced to ashes, the officials said.
They said the offices located on the first floor include Director General Accounts and Treasuries, Forest department, Technical Education and Higher Education departments.
The ground floor of the building houses the CRPF deployment, communication equipment of the police deployment incharge of security of the complex, the estates department, medical dispensary and the office of Joint Development Commissioner, the officials said.
Chief Minister Omar Abdullah visited the gutted office block for a first hand assessment of the damages.
Omar directed making alternate arrangements for the accommodation of affected departments and for ensuring safety of the retrieved records, the officials said.
In a Twitter post, Omar said the cause of the fire and the extent of the damage, particularly of records stored in the offices at the annexe will take some time to assess.