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 from patrolling in Banca Strait 15 October 1689
Amsterdam, small yacht, her master Otto van Thiel transferred to the Vrijheijt 15 September 1689, decided as being incapable to laid up 16 September 1689
Arent, chialoup, arrived at Batavia coming from Macassar 1 October 1689
Beurs van Amsterdam, yacht, arrived at Batavia coming via Banda and Amboina via Ternate 11 October 1689
Blauwenberg, small yacht, arrived at Batavia coming from the West Coast of Sumatra 19 September 1689
Blauwenhulck, ship destined towards Japara 1 September 1689, arrived at Batavia coming from Japara 7 October 1689
Boswijk, yacht, mentioned as being in Sunda Strait 9 September 1689, arrived at Batavia coming from patrolling in Banca Strait 28 September 1689, destined via Malacca towards Bengal 25 October 1689
Cadirij, small yacht, arrived at Batavia coming from Timor 17 October 1689
Capelle, yacht, arrived at Batavia coming from Cheribon with a cargo of rice and pepper 23 September 1689
Casteel Batavia, chialoup, also called yacht, departed Batavia towards Sunda Strait with a letter for the Schielant, arrived at Batavia coming back from the Schielant in Sunda Strait 10 September 1689, departed Batavia towards Sunda Strait 28 September 1689, arrived at Batavia coming with letters from the Schouwen in the Sunda Strait 2 October 1689, destined Batavia towards Persia 4 October 1689, sent towards the Dregterlant with a letter 20 October 1689, arrived at Batavia coming from the Dregterlant 22 October 1689
China, ship, destined via Ceylon toward the Netherlands 15 September 1689
Civetkat, small fluyt, arrived at Batavia coming without a cargo from Malacca 31 October 1689
Coevorden, ship, departed Batavia towards Persia 4 October 1689
Coninck van Bantam, yacht, arrived at Batavia coming from Palembang with a cargo of 3354 picols black pepper 30 September 1689, destined towards Palembang 29 October 1689
Doradus, chialoup, arrived at Batavia coming from Timor 17 October 1689
Dregterlant, ship, chamber Enkhuizen, mentioned as coming from the Netherlands 20 October 1689, arrived at Batavia coming via Cape of Good Hope from the Netherlands, 169 men 25 October 1689, same date destined towards Ceylon and to transfer master Otto van Thiel of Marken and other officers of the yacht Purmer to the Dregterlant 25 October 1689
Elisabeth, small ship, destined towards Japara 19 September 1689
Europa, retourship, departed via Ceylon towards the Netherlands 10 October 1689
Faam, yacht, destined towards Bantam to replace the Zijp 1 September 1699, arrived at Batavia coming without pepper from Bantam 4 October 1689
Grijpvogel, small yacht, departed Batavia towards Bantam 24 September 1689, arrived at Batavia coming from Bantam 15 October 1689, destined via Bantam towards West Coast of Sumatra with the radjas Hitam and Mahariadia Indra 27 October 1689
Hendrik Mourits, destined towards Siam 5 September 1689
Hengelaar, chialoup, destined towards Cheribon to inspect the projected watersawmill 9 October 1689, arrived at Batavia coming from Cheribon 24 October 1689
Hogergeest, yacht, destined towards the West Coast of Sumatra 15 September 1689, ordered to transport Radja Hitam of Troessang and Quitchil, son from Panglima Radja destined towards the West Coast of Sumatra 27 September 1689, destined towards the West Coast of Sumatra with Radja Quitchil 12 October 1689
Jambij, yacht, arrived at Batavia coming from Ternate 25 October 1689
Land van Schouwen, also called Schouwen, arrived at at Batavia coming from the Netherlands with 254 men 5 October 1689
Leck, ship, departed Batavia via Malabar and Ceylon to the Netherlands 22 September 1689
Macassar, chialoup, arrived at Batavia coming from Japara 15 September 1689
Meerl, small fluyt, arrived at Batavia coming via Palembang from Malacca with a cargo of pepper 15 October 1689, destined via Jambij towards Palembang 30 October 1689
Meijblom, pantjalang, arrived at Batavia coming from Cheribon 8 September 1689
Naerdermeer, kat, arrived at Batavia coming via Japara from Banda with a cargo of wood work from Japara 30 September
Odijck, yacht, arrived at Batavia coming from Japara 28 October 1689
Pijlswaart, yacht, decided to call her back from Sunda Strait 13 September 1689, arrived at Batavia coming from patrolling in Sunda Strait 27 September 1689
Purmer, yacht, mentioned 25 October 1689
Raap, (small) yacht, arrived at Batavia coming from Palembang with a cargo of pepper 17 September 1689, destined towards Bantam with a cargo of woodwork 11 October 1689
Schielant, ship, chamber Amsterdam, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 254 men 14 September 1689
Snauw, small yacht, destined towards the river Craoang to patrol for pirates 1 September 1689, decided to call her back from Craoang 6 September 1689, arrived at Batavia coming from Craoang 7 September 1689, decided to sent her with 2 pantjalangs towards Soerabaja 16 September 1689, departed Batavia via Cheribon towards Japara to patrol in the Trend of Madura 27 September 1689
Snobber, also called Jonge Snobber, galliot, arrived at Batavia coming from Sunda Strait 10 September 1689, mentioned 29 September 1689
Sparwouw, fluyt, arrived at Batavia coming from Banda 7 October 1689, destined towards the East Coast of Java 12 October 1689, departed Batavia towards Japara 21 October 1689
Stompneus, pantjalang, departed Batavia towards Bantam 30 September 1689
Tuijtappel, chialoup, arrived at Batavia coming from Malacca 17 September 1689
Vergulde Vlamingh, galliot, chamber Amsterdam, 15 men, departed towards Malacca ? 31 October 1689
Vlieger, chialoup, arrived at Batavia coming from Bantam 2 September 1689
Voetboog, fluyt, chamber Amsterdam, arrived at Batavia coming from the Netherlands 5 October 1689
Vrijheijt, ship, destined towards Tegal 13 September 1689, master Otto van Thiel of the Amsterdam transferred to the Vrijheijt 15 September 1689, destined via Cheribon towards Tegal 23 September 1689
Walenburgh, fluyt, arrived at Batavia coming from Japara 29 September 1689
Wapen van Tertholen, ship, destined towards Japara 7 September 1689
Westeramstel, fluyt, destined towards Japara with an enforcement of inland soldiers 6 September 1689, arrived at Batavia coming via Cheribon from Japara with a cargo of woodwork 17 October 1689
Zara, called the kings' small ship, destined towards Siam 5 September 1689
Zijp, yacht, the Faam was destined towards Bantam to replace the Zijp 1 September 1689, arrived at Batavia coming from Bantam 9 September 1689, destined towards Japara for a cargo of wood and rice 20 September 1689, destined towards Japara with 100 soldiers 6 October 1689, departed Batavia towards Japara 7 October 1689
Zonvis, also called Sonvisch, pantjalang, arrived at Batavia coming from Bantam and sent back towards same destination 21 October 1689, arrived at Batavia coming from Bantam 25 October 1689