The National Archive of Indonesia published on her website tables of contents of the so-called Daghregisters (Daily accounts) of the Castle Batavia, HR no.2518. Unfortunately they are in Dutch. In those tables you can find for instance information about the ships arriving at and departing from Batavia (nowadays Djakarta). I extracted the movements of the ships and vessels owned by the E.I.C. The dates mentioned below in the text are the register dates. See also on this weblog the notes dealing with cargo capacities and individual ships.
The civilian carpenter Jurriaan Abrahamsz left via Japara towards Rembang with a letter for the servant at Japara reporting that Abrahamsz was to built 18 new vessels 15 December 1698
America, British ship, departed Batavia towards England 10 December 1698
Bekesteijn, small frigates, destined towards the Netherlands 12 December 1698
Dieren, fluyt, arrived at Batavia coming from Japan 10 December 1698, ordered towards the Netherlands 15 December 1698
Driebergen, fluyt, departed Batavia towards the Netherlands 24 December 1698
Den Eenhoorn, ship, chamber Zealand, arrived at Batavia coming from the Netherlands 14 December 1698
Goa, chialoup, departed Batavia towards Macassar 23 December 1698
't Huijs te Loo, fluyt, chamber Zealand, departed Batavia towards the Netherlands 16 December 1698
Java, ship, arrived at Batavia coming via Tagal from Japara 12 December 1698
Johor, chialoup, arrived at Batavia coming via Tagal from Japara 15 December 1698
Mackereel, pantjalang, arrived at Batavia coming from Tanjongpoura with the 22 slaves 5 December 1698
Nieuwburg, fluyt, ordered towards the Netherlands 16 December 1698
Oostvoorn, yacht, arrived at Batavia coming from Siam [Thailand] 31 December 1698
Pool, frigate, departed Batavia towards the homeward bound fleet 6 December 1698, arrived at Batavia coming from the Sunda Strait 14 December 1698
Purmer, yacht, arrived at Batavia coming from Siam [Thailand] 31 December 1698
Snobber, galliot, departed Batavia towards Cheribon 20 December 1698
Soldaat, frigate, departed Batavia towards the homeward bound fleet 6 December 1698, arrived at Batavia coming from the Sunda Strait 14 December 1698
Spare, yacht, mentioned as left behind at Japan 10 December 1698
Swaag. fluyt, arrived at Batavia coming from Bengal 9 December 1698
Tamboer, small yacht, decided to send with a cargo of fresh tea to cape of Good Hope 13 December 1698, departed Batavia towards Cape of Good Hope 24 December 1698
Vogelstruijs, pantjalang, arrived at Batavia coming from Tanjongpoura with the 22 slaves 5 December 1698
William and Richard, British ship, departed Batavia towards Banjer 27 December 1698