Question: What should employers do if the only ID number they have for an employee is an Individual Taxpayer Identification Number (ITIN), and not a Social Security Number (SSN)?
Answer: If you must complete a W-2 without an SSN, write “Applied For” on paper copies and put all zeros in electronic files. If software programs don’t allow all zeros, the W-2 will be processed with the ITIN, but the employee’s earnings will go into the Earnings Suspense File, and won’t be credited to his/her account.
The best course of action is for the employer and employee to clear up the problem before W-2s are issued.
(Source: Social Security Administration)