The decision was taken during a cabinet meeting chaired by Chief Minister Omar Abdullah.
Work in the civil secretariat, the seat of the government housing the offices of the chief minister, ministers and senior government officers was inundated by flood waters during the early hours on September 7.
The road leading to the secretariat building was also flooded.
The secretariat building is now being de-watered and cleaned up ahead of its re-opening.
The cabinet also cancelled all Saturday, Sunday holidays in the state government offices in Kashmir Valley barring educational institutions till the closure of the offices in summer capital Srinagar when the offices move to winter capital Jammu in late October.
The state government had drawn a lot of flak on account of its dereliction to help the people hit by the floods in rescuing them or providing relief.
In another decision, the state cabinet decided to divide summer capital Srinagar into three zones for effective post flood municipal services.
The decision follows reports of accumulation of animal carcasses and debris across the city and urgent need to clean the city up to prevent an outbreak of epidemics.
The three zones will be headed by senior government officers.