can a builder build apartment above water tank???

There is nothing wrong in constructing a building over the water tank unless and otherwise it shown in the Plan approved by the CMDA that the land is being built overthe water tank

No. Apartment over water tank can be objectionable. Some times structure may tilt if under ground storage tank leaks. I think Municipal authorities or Urban development authority may not know the underground storage tank location.

Try to find out your city building bylaws, Rules or Acts as well as your CMDA Rules in the matter.

This is not a legal quarry. It relates with building plan. Why did you accepted your flat if the position exists there prior to your purchase. Once you accpeted, you lose your right to agitate at further stage.

kindly contact Muncipal authorities for solving ur problem