I went through S to N, but the procedure should be the same. Find the Canal authority office in Colon. Any taxi driver will know it. Wander in and tell the first person you see that you want to transit. Bring your passport, boat doc and all the accumulated clobber of officialdom you have collected so far. You'll probably not need any of it, but it doesn't hurt. They'll schedule a time and place to send the admeasurer--for me it was next day. If you're not in the Shelter Bay Marina, they'll want to meet you in anchorage area "F". The admeasurer, who speaks English
, will measure your boat, fill out all the paperwork, and tell you where to sign. He'll give you a form to take to the bank along with cash (for my boat, 37' admeasured length, it was 1,500 dollars), which you deposit, collecting the receipt. Then you phone
(it's a dime) the authority on the next business day when your payment has posted, and they schedule your transit. Sometimes it's next day, sometimes longer. Be prepared to get postponed a day or two at the last minute--they'll tell you the night before if you bother to call and confirm, which I recommend.
These things might have changed from 2010 when I transited, but whether it's necessary to check into and out of Colon with the local harbormaster (if you've already entered Panamanian waters), and secure a zarpe to Panama
city from Colon is up to whether the harbormaster catches you, since he's the only one who thinks this bit is necessary. He makes a good bit on his "Fines", which if you ask any canal authority people (who are a different branch of things) are ludicrous. Many boats never contact him at all, being "in transit", and do nothing illegal by it. But again, be aware that Panama
has the most convoluted, inconsistently applied rules and most corrupt officials we ever encountered, even counting Mexico
, who'se corrupt antics are monumental.