Chief Secretary Mohammad Iqbal Khanday told the employees that they needed to help mitigate the problems caused by the unprecedented floods that have claimed more than 200 dead.
Action will be taken against those who defy the directive, an official statement said.
Government offices, educational institutions and banks are shut across Srinagar and other flood affected areas.
The civil secretariat in Srinagar was also flooded. Flood water also entered the assembly complex.
The roads leading to the civil secretariat are submerged.
Flood waters also entered the police headquarters and the police control room.