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.
Aardenhout, small yacht, arrived at Batavia coming via Tegal from Japara 30 June 1689
Adrichem, fluyt, destined via the West Coast of Sumatra towards Bengal 6 May 1689, departed Batavia via the West Coast of Sumatra towards Bengal 15 May 1689
Bagger, pantjalang, arrived at Batavia coming from Sunda Strait without letters 5 June 1689, sent same day towards the Snauw in Sunda Strait 5 June 1689
Bhaeren, also called Baren, fluyt, destined towards Bengal with silver 6 May 1689, departed towards Bengal 22 June 1689
Blauwenhulck, ship, arrived at Batavia coming from Indermaijoe with wood and letters 7 May 1689
Boswijk, yacht, arrived at Batavia coming from Bengal 22 May 1689
Bruijnvis, small yacht, arrived at Batavia coming from Banda with a cargo of mace 10 June 1689, destined towards the West Coast of Sumatra 28 June 1689
Castricum, yacht, destined towards Japan 3 May 1689, decided to replace Bartholemeus Targier as master by Jan Ammans 10 May 1689
Cevetkat (=Civetkat), fluyt, departed towards Bantam 30 June 1689
Claverblat, fluyt(ship), destined towards Ceylon with rice and cash 6 May 1689, departed towards Ceylon 22 June 1689
Couwerve, ship, replaced by the Sumatra and Zijp for destination Bantam due she was 'afgevaren' (not suitable for more voyages) 14 June 1689
In 1686 she was found only to be used for some time left for service off the East Coast of Java and elsewhere.
Craanvogel, small yacht, mentioned as being in Sunda Strait 29 June 1689
Drakesteijn, fluyt, arrived at Batavia coming from Bengal 23 May 1689
Eemland, destined towards Aijmuij with gold 17 June 1689
Elisabeth, small ship, arrived at Batavia coming from Japara without letters 26 June 1689
Gasperdam, (small) yacht, destined towards Toncquin 3 May 1689, departed Batavia towards Toncquin 30 may 1689
Gideon, fluyt(ship), arrived at Batavia coming from Semarang 4 May 1689, destined towards Bengal with silver 6 May 1689, departed Batavia towards Bengal 1 June 1689
Grijpvogel, small yacht, mentioned as being in Sunda Strait 29 June 1689
Hendrik Mourits, ship, arrived at Batavia coming from Bantam with a cargo of pepper 4 May 1689
Hengelaar, chialoup, departed Batavia towards Sunda Strait 6 May 1689, arrived at Batavia coming from Sunda Strait 13 May 1689
Hogergeest, yacht, mentioned as being in Sunda Strait 19 June 1689, arrived at Batavia coming from Paliacatta 20 June 1689
Hollandse Thuijn, ship, destined towards Indermaijoe 17 May 1689, arrived at Batavia heavy leaking coming from Indermaijoe 8 June 1689, decided to be lay up 10 June 1689, hull sold for 820 realen 18 June 1689
This ship was in 1686 found only suitable for easy waters as the Easter Quartars, Malacca, Siam, West Coast of Sumatra, Palembang and Jambij.
Huijs te Spijk, fluyt, arrived at Batavia coming from Amboina with a cargo of spices 3 June 1689
Jonge Snoeper, galliot, chamber Amsterdam, arrived at Batavia coming from the Netherlands with 15 men 3 Jun 1689
Klipvis, pantjalang, arrived at Batavia coming from Sunda Strait with a letter from the Snauw and the Hogergeest19 June 1689
Lapland, chialoup, arrived at Batavia coming from Bantam 5 May 1689, destined towards Jambij 21 May 1689, departed Batavia via Palembang towards Jambij 1 June 1689
Macassar, chialoup, arrived at Batavia coming from Macassar 21 June 1689
Malacca, small yacht, arrived at Batavia coming from Malacca with 1000 casks copper 8 June 1689, decided to sent back wards 10 June 1689
Mastbosch, fluyt(ship), destined towards Bengal 6 May 1689, arrived at Batavia coming from Japara with a cargo of woodwork 8 May 1689, destined towards Bengal with silver 6 May 1689, departed Batavia towards Bengal 1 June 1689
Meerl, small fluyt, destined towards Malacca 21 May 1689
Montfoort, fluyt, destined via Siam towards Japan 9 May 16589
Negombo, yacht, arrived at Batavia coming from Bengal 19 May 1689
Peperthuijn, hulck, ordered to repair/make by the civilian carpenter Jurriaan Abraham 20 May 1689
Potvis, pantjalang, departed Batavia towards Bantam 7 June 1689
Princelant, fluyt, departed via Siam towards Japan 5 May 1689, decided to let her return directly from Japan without stopping elsewhere 11 June 1689
Pijlswaart, yacht, arrived at Batavia coming via Ceylon from Souratta 18 May 1689
Raap, small yacht, arrived at Batavia coming without letters or a cargo from Bantam 14 May 1689, destined towards Banca Strait for patrolling against pepper smugglers 24 May 1689
Sana?[Sara?], small yacht, arrived at Batavia coming back from Timor without completing the voyage 14 June 1689
Snauw, small yacht, arrived at Batavia coming from Sunda Strait 20 May 1689, mentioned as being in Sunda Strait 5 June 1689, mentioned as being in Sunda Strait 19 June 1689
Stompneus, pantjalang, destined towards Lampon and Banca Strait 5 June 1689, arrived at Batavia coming from Sunda Strait with letters from the Grijpvogel and Craanvogel 29 June 1689
Sumatra, destined towards Bantam instead of the Couwerve 14 June 1689, departed Batavia towards Bantam 18 June 1689
Vliegende Vis, pantjalang, arrived at Batavia coming from Bantam 15 May 1689
Vrijheijt, ship, arrived at Batavia coming from Indermaijoe 16 May 1689
Wapen van Alckmaer, ship, chamber Amsterdam, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 139 men 20 May 1689
Waveren, fluyt, arrived at Batavia coming from Bantam with a cargo of nuts and nutmeg and a letter 4 June 1689
Westbroek, fluyt(ship), destined towards Ceylon with rice and cash 6 May 1689, departed towards Ceylon 22 June 1689
Wijck op Zee, yacht, destined towards Japan and from there towards Canton 14 June 1689
Zeijlvis, pantjalang, destined towards Lampon and Banca Strait 5 June 1689
Zijp, ship, also called yacht, destined towards Indermaijoe 17 May 1689, destined towards Bantam in stead of the Couwerve 14 June 1689, arrived at Batavia coming from Indermaijoe with woodwork 30 June 1689