If your rental income is from "renting of residential dwelling for use as residence" then the same shall not be taken in consideration while calculating the limit of Rs 9,00,000/-.
The above is opined from the reading of Sec 66B which is as follows: " There shall be levied a tax (hereinafter referred to as service tax) at the rate of 12% on the value of all services, other than those specified in the negative list...."
And clause m of Sec 66D specifies "renting of residential dwelling for use as residence"
So if your rental income is from residential unit used for residential purose then it will not be considered otherwise it will be considered.