I am currently working for an NIH Agency under J1 visa, and would like to apply for Green Card under the EB1 and NIW (National Interest Waiver) categories at the same time. 

I want to ask my advisor at the agency to write a reference letter for me. Is it true that a NIH employee cannot write reference letter for Green Card application purpose.

The NIH staff members may not write letters of reference/recommendation to or for submission to another federal agency in support of visa or Green Card applications, on behalf of the NIH Agency or on NIH Agency's letterhead. But an employee should be able to his/her own personal letter on plain stationery for an alien's performance and achievement.

Also, the NIH staff members may send the requestor copies of any performance evaluations ("form of evaluation") which was previously prepared describing the person's relative skills, performance, development, etc., or copies of any letters of reference that previously wrote to evaluate his/her suitability for a job at another institution.