Why i want to pay VAT in two pleases?

Hi sir/madam, i am vijay, im working in kerala. i bought a new car from kerala for run as a taxi. i paid VAT tax in kerala at the time of purchase. my native is tamilnadu so i want to register my car in my region. agents told me about the entry tax. so i ask about this entry tax to commercial tax office (marthandam region). they told me about the calculation . they told entry tax = (total amount in invoice * 12.5 ) - VAT amount i paid in kerala. i calculate my car's entry tax in this manner and i god a amount nearly 16,000rs. but then only i know my region is not under marthandam region my commercial tax office office is in nanguneri. so i went to nanguneri office, they calculate the entry tax and told me to pay nearly 78,000. i told them about this structure(calculation i got from marthandam officer) but they replied little hardly and they never accept that. i send mail to Commercial tax head office. but i didnt get any replay from them(still today). so i don't have any other option at that time so i paid that amount by DD. i really want to know why i want to pay VAT in two pleases? VAT is under central government? is any way to get my amount back legally ? please help me. im really in trouble.