On Friday, Oct.11, the Ornithological Council asked Dept. of Interior Secretary Jewell to re-call staffers who issue permits. At least as to the Migratory Bird Treaty Act, the fees charged for permits are retained by the Division of Migratory Bird Management (by Congressional authority) and therefore, permit issuance is not dependent upon Congressional appropriations. Other federal activities that are fee-funded have continued through the shut-down and indeed, it appears that the APHIS Veterinary Services permit program may have been operational during the shut-down.
The request was sent to numerous individuals in the directorate who, based on the DOI shut-down plan, are believed to have been exempted from the shut-down.
The request also asked that to the extent that permit issuance for ESA, CITES, BGEPA, MMPA, and Lacey Act permits are fee-funded, that these employees also be re-called to work.
(Now - aren't you glad you have to pay permit fees?!)