Sounds like a nice catch! Unfortunately these types of lesions are not pathognomonic. Have you observed any lesion inside the mouth also? Have you collected any kind of sample?

Could be from contaminants. Any deep ocean outfalls (for treated sewage) in the vicinity? I'd take a biopsy and send for analysis. If you can get a tissue sample you could also check for a range of contaminants (metals, PCBs and other organochlorines). Similar lesions occur in turtles as a precursor to tumours (fibropapilloma virus).

We are preparing to collect samples for histopathological analysis and maybe bacterial culture, but there is no guarantee that we'll catch another having this pathology.  These are just two of the hundreds of sharks caught/tagged/released between two tagging efforts being conducted in about the same area.  Contaminants are a possibility but are very difficult to determine as a cause and quality analysis (using low detection levels, and including both tissue and sediment/elutriate/water analyses) are very expensive.  In the area of capture (northern Ten Thousand Islands) there is no significant outfalls in the area although I'm sure the area has its share of organochlorine pesticides and other contaminants.  

Hope that you can catch the infected ones and come up with solution to save the others. Fungal analysis would also worth to try considering the shape of lesions. But it sometimes difficult to isolate fungi from samples unless sampling collection is performed based on the standard procedures (such as collecting deep scrabing tissues and etc).

Yes, fungus, or a complex of bacterial and fungal infection, is a consideration of ours.  

Never seen something like that! I agree that it looks like fungal infection but the only way to find out is by taking biopsies. Might be worth to be alert and take a few good samples next time (if ever) your team comes accross something like that again. It looks awful by the way....

 I understand organochlorine contaminants are expensive but if you can work with a lab as a collaboration you'll get them done for nothing. It's a great post-doc project. I've started working with EnTox in Australia for the same reason and it's a mutually beneficial relationship. I help out with processing of the samples in the lab, which saves time, and I build more lab skills. I do believe contaminants play a major role in these types of immunoresponses and the more data that's collected means we get closer to providing evidence for a cause-effect relationship. This has been confirmed in other species. Just saying!

The shape and location of the lesions are suggestive of an infectious etiology.

The differential diagnosis would include a viral, bacterial, algal, protozoal or fungal etiology.

Microscopical examination of fresh smears and histological examination of biopsies would provide interesting information regarding the precise etiology in the next cases.

The following article from Vet Pathol might give you an insight of the diversity of possible diseases, and it also lists a number of interesting primary literature sources on shark skin diseases.

http://vet.sagepub.com/content/50/3/377.full