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.
Andromeda, yacht, departed Batavia towards Ternate with 20 European soldiers 1 January 1698
Boor, (small) fluyt, destined to be part of the 2nd homeward bound fleet 7 January 1698, decided that her departure would be around February 21 January 1698
Cadirij, small yacht, departed Batavia towards Soerabaja 25 January 1698
Carthago, ship, decided that her departure towards the Netherlands would be the end of January 21 January 1698
Coning van Bantam, yacht, arrived at Batavia coming from Palembang with a cargo of pepper 21 January 1698
Crab, pantjalang, arrived at Batavia from after observing the small British ship Sergeant Marchiant 9 January 1698
Dieren, fluyt, chamber Rotterdam, arrived at Batavia coming from the Netherlands 31 January 1698
Elisabeth, chialoup, arrived at Batavia from after observing the small British ship Sergeant Marchiant 9 January 1698
Faam, yacht, news of her failed voyage from Souratta towards Mocha 19 January 1698
Geelvink, small yacht, departed Batavia towards Amboyna 18 January 1698
Gent, ship, decided that her departure towards the Netherlands would be the end of January 21 January 1698
Haas, small fluyt, destined towards Banda 7 January 1698
Hobre, fluyt, arrived at Batavia coming via Mallabaar and Ceylon [Sri Lanka] from Persia 19 January 1698
Landloper, small fluyt, decided that her departure would be around February 21 January 1698
Leeuw, chialoup, decided as being worn out to sell 17 January 1698, sold 24 January 1698
Nijptang, hooker, departed Batavia towards Timor with the new chief Francois van den Ende 8 January 1698
Oostersteijn, ship, chamber Zealand, arrived at Batavia coming from the Netherlands 19 January 1698
Pampus, yacht, arrived at Batavia coming from Siam [Thailand] with on board former chief Thomas van Zon 4 January 1698
Peperthuijn, small yacht, arrived at Batavia coming from the West Coast of Sumatra 19 January 1698, departed Batavia towards Bantam with on board 12.000 Spanish realen and 3 picols cloths for the sultan 30 January 1698
Petronella, chialoup, departed Batavia towards Japara 25 January 1698
Samarang, chialoup, decided as being worn out to sell 17 January 1698, sold 24 January 1698
Schelde, yacht, destined towards Ternate 7 January 1698
Sint Pedro, Portuguese ship coming from Macao 4 January 1698
Snobber, galliot, arrived at Batavia coming from Bantam 11 January 1698
Surrabaija, also called Sourabija, chialoup, decided as being worn out to sell 17 January 1698, sold 24 January 1698
Swarten Arent, small yacht, reported as lost and crew murdered, the new chief at Timor got orders how to handle this case 8 January 1698
Voetboogh, fluyt, departed Batavia via Japara towards Banda 25 January 1698
Voorschoten, fluyt, arrived at Batavia coming via Ceylon [Sri Lanka] from Persia 24 January 1698
Wesel, galliot, destined to search for the vessels of Sumanap between this place and Cheribon 3 January 1698
Westbroek, fluyt, sold while laid up 3 January 1698
