The GBAO permit (to see the eastern half of the country and Pamirs) cost is included in the base visa cost, but you MUST ask for it separately (in person and in your processing cover letter). If you don’t have a cover letter they will give you one to copy for the request at the consulate. Make sure you come with TWO copies of your visa paperwork (and associated photos). When picking up the visa they will make you sign that the visa is correct. NOTE: the actual dates, etc are handwritten so be sure to triple check!
Cost for Americans: ¥9000 JPY (8000 for the visa + 1000 processing fee) for a 30 day single entry visa. This is paid via wire transfer (ATM) with receipt DUE AT APPLICATION TIME.
Website: Embassy of Tajikistan in Tokyo