Separating digits in an Integer
Input and validation

Using a Scanner is a good idea, and using a try-with-resources block is the right thing to do.

You don't need to close the Scanner or the underlying System.in.  The whole point of the try-with-resources block is that resources will be automatically closed for you.

Note that neither the Scanner(Readable) constructor nor Scanner.nextInt() will ever throw an IOException.  The only exception you need to catch (but didn't) is NoSuchElementException.  (Well, also InputMismatchException, but that is just a subclass of NoSuchElementException.)  Your program will crash with a NoSuchElementException if you send it an EOF at the prompt.

The error messages aren't quite right.  The first message should read: "Input should be exactly 5 digits."  The second message is unhelpful: you should tell the user what would be considered valid input.

The validation is not quite strict enough: a negative four-digit integer will also be accepted.

Output

Strictly speaking, the output is not quite right, in that you also append three spaces after the fifth digit.  On screen, the output will look the same, but if you pipe the output to a program that examines the bytes, you'll see the trailing spaces.

You don't need to call String.trim().

newString is not a good name: it's not a string, and there is no oldString.  If I had to pick a name, I'd call it digits.

Suggested solution

With Java 8, the simplest solution is to use String.join().

public static void main(String[] args) {
    try (Scanner input = new Scanner(System.in)) {
        int n = input.nextInt();
        if (!(1e5 &lt;= n &amp;&amp; n &lt; 1e6)) {
            System.out.println("Input should be exactly 5 digits.");
            return;
        }
        System.out.println(String.join("   ", String.valueOf(n).split("")));
    } catch (NoSuchElementException e) {
        System.out.println("Error: No integer was given.");
    }
}