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.
Baeren, small fluyt, arrived at Batavia coming from Bengal 13 February 1689
Beurs, yacht, destined towards Amboina 12 January 169
Blauwenhulck, ship, departed towards Samarang 4 January 1689
Bruijnvis, yacht, destined towards Banda 25 February 1689
Casteel Batavia, chialoup, departed Batavia towards Sunda Strait with a letter for the officers of the Princelant 7 February 1689, arrived at Batavia coming from Sunda Strait 8 February 1689
Castricum, ship, chamber Amsterdam, arrived at Batavia coming with Cape of Good Hope from the Netherlands with 120 men 18 February 1689
Cheribon, chialoup, departed Batavia towards Bantam 15 February 1689, arrived at Batavia coming from Bantam 19 February 1689
China, ship, destined towards Ternate 12 January 1689
Civetkat, fluyt, arrived at Batavia coming from Bengal 13 February 1689
Coeverden, ship, arrived at Batavia coming from Ceylon 10 February 1689
Eemlant, yacht, arrived at Batavia coming from Aijmuij 11 January 1689
Emmenes, fluyt, arrived at Batavia coming from Palembang with pepper 5 January 1689, destined for the Chamber Enkhuizen 11 February 1689
Gaasperdam, yacht, arrived at Batavia coming from Toncquin 18 January 1689
Geregtigheijt, chialoup, arrived at Batavia coming back from the 6 homeward bound ships anchored in or near the Sint Nicolaas Bay 3 January 1689
Gideon, fluyt, arrived at Batavia coming from Bengal 15 January 1689
Jambij, yacht, departed Batavia via Japara and Macassar towards Amboina 25 January 1689
Macasser, chialoup, departed Batavia towards Macassar 17 January 1689
Oostersouburgh, arrived at Batavia coming from the high lands of Bantam 5 January 1689, destined homeward bound 13 January 1689, apparently was master Abraham Witboom replaced 21 January 1689
Peperthuyn, small yacht, arrived at Batavia coming from Palembang with pepper 17 February 1689
Princelant, fluyt, chamber Amsterdam, arrived at Batavia coming from the Netherlands with 195 men 8 February 1689
Rog, small yacht, departed Batavia via Amboina towards Banda 23 January 1689
Snauw, small yacht, arrived at Batavia coming from Malacca 25 January 1689
Sparwoude, fluyt, destined towards Banda 12 January 1689
Sumatra, ship, arrived at Batavia coming from the West Coast of Sumatra 28 January 1689
Vrijheijd, ship, arrived at Batavia coming from Siam 2 January 1689
Westbroek, small fluyt, arrived at Batavia coming from Bengal 13 February 1689
Westeramstel, fluyt, arrived at Batavia coming from Bengal 14 January 1689, destined towards Timor 15 February 1689
Wijk op Zee, yacht, departed Batavia towards Bantam 23 January 1689, arrived at Bantam coming from Bantam with a cargo of pepper 1 February 1689
Zijp, yacht, arrived at Batavia coming via Bantam from Sunda Strait 14 January 1689
Zuid Beveland, yacht, destined homeward bound 13 January 1689, apparently was master Willem Burggraaf replaced 18 January 1689