Refund cheque with very low amount, without any intimation

I have received refund for lesser amount, i.e refund amount was 98,000 but i received 36,000 only, and that too widout any intimation or order. when i enquired in Income tax office, they told me to write an application for rectification, Please tell me what should I do? Can income tax office send such refund cheque without any intimation? I have also check tax credit to my account online and it is proper.