If an employer maintains a US qualified plan and has Puerto Rico resident employees, how does the employer go about qualifying its plan with the Puerto Rico Treasury Department? Where can one get a copy of the qualification procedure and forms?

Have fun. It's a painful process. The website for the Hacienda (Puerto Rico's Treasury department) is:

http://www.hacienda.prstar.net/

There are several schedules which must be completed for each year for which you want a qualification, as well as submitting the operative documents of the plan (trust, spd, resolutions by which the plan came into existence, etc.)

Also, my understanding is that Puerto Rico REQUIRES that a plan file for qualification in order for taxes to be deferred.

Due to the differences in the Puerto Rican and US qualification standards you will not be able to get a US Qualified plan, Qualified in Puerto Rico without SUBSTANTIAL revision. Therefore, 99% of all plan sponsors set up separate US and Puerto Rican plans.

Because most US sponsors have relatively few Puerto Rican employees, they use Prototype plans that have been qualified by the Hacienda. My general advice is to seriously consider separating the employees into two plans and use a Puerto Rican Prototype. This is the simplest and least expensive way to do this.

Good luck!