If an instrument is under stamped by accident or ignorance of the parties can it be rectified? If so what is the procedure?

YES. There is provision to rectify the mistake. Section 41 of Indian stamp act and section 40 of Karnataka stamp act provides for such situations. The time limit is one year from the date of execution. But this relief is not applicable for promissory note, bill of exchange; instrument attracting stamp duty of 15 paisa or less and mortgage of crop. The concerned parties on his own by producing the document, may bring it, to the notice of the Collector or Dist. Registrar, the fact that the instrument is under stamped and agrees to pay the amount of the shortfall. If the Collector or Dist. Registrar is satisfied that the instrument is under stamped by accident, mistake or urgent necessity, he may permit the party to pay the correct stamp duty and shall certify to the that effect.