I don't think scanner.delimiter will work for this kind of problem. 
If you have quotes in the data where the extra comas exist, you can either use a regular expression or code to solve this kind of problem using also the String.split as mentioned in similar answers/questions.
If you don't have quotations, then there is really nothing you can do.
There have been similar examples on stackoverflow. 
For example I think this one applies to you:
Splitting a csv file with quotes as text-delimiter using String.split()
Using Split
public static void main(String[] args) {
    String s = "Sachin,,M,\"Maths,Science,English\",Need to improve in these subjects.";
    String[] splitted = s.split(",(?=([^\"]*\"[^\"]*\")*[^\"]*$)");
    System.out.println(Arrays.toString(splitted));
}
Using custom code
public static ArrayList<String> customSplitSpecific(String s)
{
    ArrayList<String> words = new ArrayList<String>();
    boolean notInsideComma = true;
    int start =0, end=0;
    for(int i=0; i<s.length()-1; i++)
    {
        if(s.charAt(i)==',' && notInsideComma)
        {
            words.add(s.substring(start,i));
            start = i+1;                
        }   
        else if(s.charAt(i)=='"')
        notInsideComma=!notInsideComma;
    }
    words.add(s.substring(start));
    return words;
}