[hardwired]

Some ideas. You could read the file, counting the number of lines, make your two-dimensional array with the number of lines. Then read it again and split each line into an array of Strings and parse each one to an int for the line array of ints.
Or you could start with a zero-length array, read the file once, parse each line to ints for the line array and add it to the array.
Or you could read the entire file as a string, count the number of lines and proceed as before.
You could use a BufferedReader or a Scanner for reading the file.

Code:

// Zero-length array
int[][] arrayOfInts = new int[0][];
// Split a String
String line = reader.readLine();
String[] tokens = line.split("\\s");
You could use a BufferedReader for the above or a Scanner.
// Add a line array to the array
int len = arrayOfInts.length;
int[][] temp = new int[len][];
System.arraycopy(arrayOfInts, 0, temp, 0, len);
temp[len] = newLineArray;
arrayOfInts = temp;
// For a BufferedReader
BufferedReader br = new BufferedReader(
                    new InputStreamReader(
                    new FileInputStream(arg)))