No charge for small crews. However there are some prohibited matters for shooting. Minimum 1 week to get their permit.
Tokyo Sky Tree
Film-crew friendly location, no film fee. Entrance fee to observatory will be waived. You can interview PR person. Minimum 1 week to get their permit.
If your script contributes its promotion, they do not charge you. Otherwise film fee 16,200yen will apply. You must pay entrance fee to observatory. Minimum 1 week to get their permit.
Imperial Palace Outer Garden
They do not charge you. Number of crew is restricted within 5, large film crews are not allowed. Normally 3-4 days to get their permit.
Tuna Auction at Toyosu Fishmarket
There is a certain place for filming, you will have to shoot through glass window. Auction starts from 05:30am. You can interview PR person. Minimum 1 week to get their permit.
Outer Fishmarket at Tsukiji
There are many rules to film at this place. Depending on where you shoot, you must obtain police permit which costs you 2,100 yen. Minimum 2 weeks to get their permit.
Scramble Crossing at Shibuya
You cannot get official permit here, but many foreign crews get away here without permit. Police will not disturb you unless you disturb public. Shooting with tripod could make problem.
Yakatabune Boat(dinner cruise)
Fixed-price of 11,000 yen per person includes dinner. If your script is considered as their promotion, some boat company could give you complementary ride.
Kawaii Monster Cafe at Harajuku
They charge 20,000 yen film fee, but you have a chance to get it free depending on your script and shoot time. If you need food and drinks, they will charge you film fee.
Sumo stable morning practice
They do not charge you at all, but long and complicated procedures needed. Some period of the year they do not allow filming. You must apply for permit at least 1 month before shooting.