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. 2519. 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.
Andromeda, small yacht, destined towards Bantam 11 December 1699, arrived at Batavia coming from Bantam 22 December 1699
Baros, chialoup, arrived at Batavia coming from 1 December 1699
Bije, small yacht, mentioned 29 December 1699
Casteel Batavia, galliot, mentioned 29 December 1699
Donkervliet, ship, mentioned 6 December 1699
Eijkelenburg, frigate, arrived at Batavia coming from Bengal 21 December 1699, destined to transport the trade books of Batavia to the Netherlands 26 December 1699
Emmenes, small fluyt, arrived at Batavia coming from the West Coast of Sumatra 30 December 1699
Faam, yacht, mentioned 29 December 1699
Geregtigheijt, chialoup, destined towards Macassar 29 December 1699
Goudesteijn, ship, tidings from Siam of her arrival at Ligor 24 December 1699
Hobre, fluyt, arrived at Batavia coming from Choromandel 2 December 1699, departed Batavia towards Bantam 19 December 1699
Hen, small fluyt, arrived at Batavia coming from Ceylon [Sri Lanka] 23 December 1699, destined towards Cape of Good Hope 26 December 1699
Herderinne, yacht, mentioned 29 December 1699
Hoen, galliot, arrived at Batavia coming via Mallabaar from Souratta 22 December 1699
Java, ship, hull sold 4 December 1699
Merensteijn, ship, destined towards the Netherlands 15 December 1699, departed Batavia 17 December 1699
Oostvoorn, small yacht, destined towards Bantam 14 December 1699, arrived at Batavia coming from Bantam 22 December 1699
Overrijp, fluyt, destined towards the Netherlands 15 December 1699, departed Batavia 17 December 1699
Pampus, yacht, arrived at Batavia coming from 5 December 1699
Parkiet, vessel, departed Batavia towards Tanjongpoura 20 December 1699
Petronella, chialoup, arrived at Batavia coming from Japara 16 December 1699
Princeland, fluyt, tiding of her arrival at Bantam 4 December 1699, arrived at Batavia coming from Bantam 9 December 1699
Pruijm, galliot, mentioned 29 December 1699
Ridder des Augiers, French ship, departed Batavia towards Souratta 2 December 1699
Salland, ship, mentioned as being in worse condition 2 December 1699
Schelde, yacht, arrived at Batavia coming from Cheribon 12 December 1699
Susanna, small yacht, arrived at Batavia coming from Bengal 22 December 1699
Waelstroom, ship, arrived at Ansuanij despite the fear she was lost 21 December 1699