I was discussing this with Eusstass, but he hasn't replied in a few weeks, so I'm submitting this to everyone's attention. Below I'll paste my current conclusion on the matter.

Sadly, the native speaker I hoped would provide the answer has not replied yet (you can see the thread I made here, someone else has responded with the raws but I don't know them well). For the moment, going by what we know, I would say the two agencies are distinct:

  • The International Environmental Permit Agency (国際環境許可庁, kokusai kankyō kyoka-chō), translated by Viz as International Environmental Agency (344) coordinates the IVPA agencies and it should be the on glasses guy is working for, since he's told to do just that (341). So we could name him the IEPA Deputy Secretary. Also, it's the agency in whose base are stored the 5 GC's victims (344).
  • The International Voyage Permit Agency (国際渡航許可庁, kokusai tokō kyoka-chō), translated by Viz as Restricted Voyage Agency (341) and International Permit Agency (359), is an agency under the control of of V5 (340). There is one in each continent (340, 341). Glasses guy coordinates all of them through his own agency (341). Also, the head of all 5 agencies (or one of the 5 leaders?) is an official survivor of the DC (359). 

To piece this info together, I compared the Viz and unofficial translations and used the info from the raws you gave me. I'm far from 100% sure I'm correct, but this seems to be the most reasonable scenario now. So I'd say we go for it; if we're wrong, someone will correct us later on, it might be easier to get confirmation that way. The first thing I'd do is create an article for each agency, and only later one for the IEPA guy. Since that's what we always done, though, we should use the Viz translations for the titles, and report the exact meaning in a parenthesis. So the three pages would be named:

  1. International Environmental Agency (IEA)
  2. Restricted Voyage Agency (RVA) or International Permit Agency (IPA; Viz has used both, so which one do you prefer?)
  3. IEA Deputy Secretary (Glasses guy)

What do you think? There still might be a few dark areas, but it appears certain that the two agencies are distinct.