Turn off the the Thousand Separator and Decimal Separator in WC Settings, then try this code in your functions.php
add_filter( 'formatted_woocommerce_price', 'wc_indian_price_html', 100, 1 );
function wc_indian_price_html( $price ){
$explrestunits = "" ;
if(strlen($price)>3){
$lastthree = substr($price, strlen($price)-3, strlen($price));
$restunits = substr($price, 0, strlen($price)-3); // extracts the last three digits
$restunits = (strlen($restunits)%2 == 1)?"0".$restunits:$restunits; // explodes the remaining digits in 2's formats, adds a zero in the beginning to maintain the 2's grouping.
$expunit = str_split($restunits, 2);
for($i=0; $i<sizeof($expunit); $i++){
// creates each of the 2's group and adds a comma to the end
if($i==0)
{
$explrestunits .= (int)$expunit[$i].","; // if is first value , convert into integer
}else{
$explrestunits .= $expunit[$i].",";
}
}
$thecash = $explrestunits.$lastthree;
} else {
$thecash = $price;
}
return $thecash;
}