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.'s 2504-2505. 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.
Aap, store vessel, destined towards Tanjongpoura 6 August 1689
Aardenhout, small yacht, departed Batavia towards Sunda Strait 2 July 1689, ordered to patrol in Banca Strait watching for a small French ship expected from Phodecherij 2 August 1689, ordered to patrol in Banca Strait watching for a small French ship 7 August 1689
Bagger, pantjalang, departed Batavia towards Sunda Strait 29 July 1689, arrived at Batavia with a letter from the Zion 14 August 1689
Blauwenhulck, ship, departed Batavia towards Bantam with a cargo gunpowder 11 August 1689, arrived at Batavia coming from Bantam with bookkeeper general Paulus de Roo 25 August 1689
Boswijk, small yacht, ordered to patrol in Banca Strait watching for a small French ship expected from Phodecherij 2 August 1689, ordered to patrol in Banca Strait watching for a small French ship 7 August 1689
Bruijnvis, small yacht, destined towards the West Coast of Sumatra 6 August 1689
Capelle, yacht, mentioned 17 August 1689, destined towards Cheribon 19 August, departed Batavia towards Cheribon 28 August 1689
Casteel van Batavia, yacht, also called ship, arrived at Batavia coming via Macassar from Amboina with a cargo of cloves 19 July 1689, destined towards Persia 19 July 1689, departed Batavia towards Sunda Strait with a letter for the Nieuw Nederlant 28 July 1689, arrived at Batavia coming from Sunda Strait 1 August 1689, departed Batavia towards Sunda Strait with a letter for the Zion 12 August 1689, arrived at Batavia coming from the Zion in Sunda Sunda 15 August 1689
Castricum, yacht ship, departed Batavia towards Japan 2 July 1689
Cheribon, chialoup, departed Batavia towards Craoang for patrolling 27 August 1689
China, ship, arrived at Batavia coming from Ternate 8 August 1689
Civetkat, small fluyt, arrived at Batavia coming from Bantam with a cargo of pepper 15 July 1689, destined towards Malacca 19 July 1689, departed Batavia via Jambij and Palembang towards Malacca with the representatives of the king at Jambij 6 August 1689
Coninck van Bantam, yacht, arrived at Batavia coming from Palembang with a cargo of pepper 1 July 1689, destined towards Palembang 19 July 1689, departed Batavia towards Palembang with the representatives of the king 25 July 1689
Couverden [=Coeverden], ship, destined towards Persia 19 July 1689
Couwerve, ship, arrived at Batavia coming from Bantam 5 July 1689, decided to her sell for as much as possible 8 July 1689, hull sold for 620 rijksdaalders 13 August 1689
Craenvogel, small yacht, mentioned 19 July 1689
Drakesteijn, destined towards Bengal 29 July 1689, departed Batavia towards Bengal 21 August 1689
Eemlant, yacht, departed Batavia towards Aijmuij 4 July 1689
Elisabeth, small ship, arrived at Batavia coming from Japara 30 August 1689
Faem, yacht, arrived at Batavia coming from Jaffanapatnam 21 August 1689
Grijpvogel, small yacht, mentioned 19 July 1689, arrived at Batavia coming via Bantam from Sunda Strait 8 August 1689
Hendrik Mourits, destined towards Siam 29 July 1689
Hengelaar, chialoup, departed Batavia towards Craoang for patrolling 27 August 1689
Huijs te Spijk, destined towards Souratta 19 July 1689, destined towards Souratta 5 August 1689, master Jan Gerrits transferred to the [Nieuw] Nederlant to replace Marcelles Kock 12 August 1689, departed Batavia towards Souratta 26 August 1689
Leck, ship, arrived at Batavia coming via Tutucorijn from Souratta 17 August 1689, destined via Malabar and Ceylon towards the Netherlands 19 August 1689
Lijster, hooker, arrived at Batavia coming from Ternate without letters 15 August 1689, laid up as being incapable 19 August 1689
Macassar, chialoup, destined towards Bantam 15 July 1689, arrived at Batavia coming from Bantam 9 August 1689, departed Batavia via Cheribon towards Japara 20 August 1689
Malacca, small yacht, departed Batavia towards Malacca 23 July 1689
Meijblom, pantjalang, arrived at Batavia coming from Japara 18 July 1689, departed Batavia towards Cheribon 1 August 1689
Negombo, yacht, destined to leave with the Sint Martensdijk and the British small ship Dorothe Sunda Strait 19 July 1689, arrived at Batavia coming back from her convoy duty of the Dorothe 1 August 1689, destined towards Bengal 9 August 1689
Nieuw Nederlant, ship, chamber Amsterdam, mentioned 28 July 1689, arrived at Batavia coming via Cape of Good Hope from the Netherlands, 249 men 1 August 1689, master Marcelles Kock replaced by Jan Gerrits 12 August 1689
Pepertuijn, small yacht, also called hulk, arrived at Batavia coming via Jambij from Palembang 9 August 1689, destined towards Palembang 19 August 1689, departed Batavia towards Palembang 23 August 1689
Pijlswaert, small yacht, ordered to patrol in Sunda Strait watching for a small French ship expected from Phodecherij 2 August 1689, departed Batavia towards Sunda Strait 7 August 1689
Purmer, yacht, arrived at Batavia coming from Jaffanapatnam 25 August 1689
Raap, small yacht, mentioned 5 July 1689, decided to let her return from Banca Strait 15 July 1689
Sint Martensdijk, yacht, destined to leave with the Negombo and the British small ship Dorothe Sunda Strait 19 July 1689, arrived at Batavia coming back from her convoy duty of the Dorothe 1 August 1689, ordered to transport 3 British from the Royal James towards Coromandel 12 August 1689, departed Batavia towards Coromandel 21 August 1689
Snauw, small yacht, arrived at Batavia coming from Sunda Strait 7 July 1689, arrived at Batavia coming from Sunda Strait 19 July 1689
Snobber, galliot, ordered to patrol in Sunda Strait 8 July 1689, destined via Bantam towards Sunda Strait 11 July 1689
Steenbrasem, pantjalang, departed Batavia towards Cheribon 3 July 1689, arrived at Batavia coming from Cheribon 17 July 1689, departed Batavia towards Sunda Strait 20 July 1689
Sumatra, destined via Ligor towards Siam 29 July 1689, arrived at Batavia coming from Bantam 8 August 1689
Tertholen, yacht, arrived at Batavia coming via Malacca and Palembang from Tanaserrij with a cargo of timber, tin and pepper 27 July 1689
Vlieger, chialoup, departed Batavia towards Bantam 27 August 1689
Walenburgh, fluyt, decided to sent with inland soldiers towards? 26 July 1689, arrived at Batavia coming via Malacca from Bengal 1 August 1689, destined towards Japara with cash money 25 August 1689, departed Batavia towards Japara 28 August 1689
Wapen van Alckmaar, also called Alkmaar, destined towards via Coromandel and Ceylon the Netherlands 5 July 1689, ordered to load 10 picols pepper on board 12 July 1689, destined towards Coromandel with order to visit Ceylon 3 August 1689, destined towards Coromandel and from there via Ceylon towards Europe 6 August 1689
Waveren, ship, destined towards Bengal 9 August 1689
Westeramstel, fluyt, arrived at Batavia coming from Timor 26 July 1689, decided to sent with inland soldiers towards? 26 July 1689, destined towards Japara with cash money 25 August 1689
Wijck op Zee, yacht ship, departed Batavia towards Japan 2 July 1689
Zeijlvis, pantjalang, mentioned 5 July 1689
Zijp, yacht, departed Batavia towards Bantam with book keeper general Paulus de Roo 31 July 1689
Zion, ship, chamber Delft, mentioned as being in Sunda Strait 12 August 1689, arrived at Batavia coming from the Netherlands, 184 men, 16 August 1689