Having a social security number is NOT a legal requirement to be permitted to work in the USA. A J1 intern is allowed to legally start working as soon as they arrive in US and before they have their SSN. All they need to show you is their legal work documents and the I-9 is filled out within 3 days of the intern's hire date. The intern/trainee should also be able to provide you with proof of submitting their application for a social security number for your records.
Sometimes it is challenging to actually pay an intern through your payroll system, without the number. Some hotels create an SS number like 000-00-0012 SS. In circumstances when an intern is forced to go for a lengthy period of time without a SSN for any number of reasons, if you can work out something whereby the J1 intern can receive some or all of their pay check owed in cash until we can process an actual pay check. When the pay check processes, it will contain pay for all of their past work less the amount he already received in cash.
If you receive the SSN after filing your wage reports to the IRS, file a form W-2c (Corrected Wage and Tax Statement). Visit www.ssa.gov for instructions.
E-Verify
Regarding filling out the E-verify the following states: Pg. 17 #4
http://www.uscis.gov/USCIS/Verification/E-Verify/E-Verify_Native_Documents/manual-employer_comp.pdf
IMPORTANT: If you select ‘An alien authorized to work’ you may also be required to indicate that you are entering either the Alien number or I-94 number from the employee’s Form I-9. Then it prompts to asking why the SSN wasn’t provided and Pg. 17 #5 states: If an E-Verify case is not created by the third business day after the employee begins work for pay, the user must indicate the reason for the delay. Select: Awaiting Social Security number