I would follow the rules. We didn't in 2010 (unintentionally) and wound up in some trouble.
When we visited
Indonesia in 2010 the CAIT cruising
permit process was in force. We obtained one while in Langkawi. Now there is a newer process, the Yacht Electronic
Registration System. Information on this system is available on Noonsite. A VISA is also required.
We did understand that
Indonesia required a VISA but we understood that we could obtain a visa on arrival.
We sailed to an Indonesian port of entry on Sumatra Island and anchored. Calling on the
radio we were instructed to bring a boatload of very polite, uniformed, officials, to our
boat (I ferried them in the dingy). Everything was fine until they asked for our Visas. Turned out that Visa on arrival was only available at an international
airport. We went to shore and reported to the Port
Captain. The next thing we knew we were in the back of a big black SUV going we had no idea where. At some other facility they put us in a room and shut the door. Then they told us we were in the country illegally and wanted us to surrender our passports. Judy cried and they fled the room (LOL). Then they told us we could keep our passports but had 24 hours to get out of the country, which we did, and they put a guy personally in charge of us to supervise our presence until we left. It was pretty clear that while they were polite and treated us with a degree of kindness, they were totally serious and formal.
We returned to Lankawi and a few months later reapplied for visas and a new CAIT, which were both granted, and this time our visit was completely pleasant and normal.
We actually loved Indonesia, very much, but we don't recommend fooling around with their rules.