The downpour has left the chambers of at least three ministers soaking as water leaked through the roof.
The false ceiling broke at several places while rain water seeped into the stamps and registration section of the revenue department.
All these are housed in block-4 of the secretariat complex.
State Municipal Administration Minister P Narayana, who oversaw the construction of the complex, sought to play down the matter saying "some small problems are always common."
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Last month, the rain water leaked into the chamber of opposition leader YS Jaganmohan Reddy in the Legislature building, located in the same compound.
The state government then called it an act of 'sabotage' and ordered an inquiry by the Crime Investigation Department (CID), which is yet to be concluded.
The maintenance staff plunged into action to mop up the rain water while the revenue department staffers hurriedly removed the files, computers and other material to safety as the ceiling cracked.
"When you build a house, there will be problems. You need not see them with a magnifying glass," the minister said, adding that there was nothing amiss with the construction.