The National Archive of Indonesia published on her website tables of contents of the so-called Daghregisters (Daily accounts) of the Castle Batavia. 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 25 May 1688, arrived at Batavia coming from Tanjongpoura 10 June 1688
Aardenhout, small yacht, destined to patrol along Java 18 May 1688
Blaeuwen Hulck, ship, arrived at Batavia coming via Japara from Bima transporting woodwork from Japara 13 June 1688, destined towards Bantam 24 June 1688
Bombain, yacht, destined towards Bengal 18 May 1688
Boswijk, small yacht, destined towards Japan 18 May 1688, departed Batavia towards Japan 27 June 1688
Casteel Batavia, yacht, arrived at Batavia coming from Amboina 2 June 1688
Cheribon, chialoup, destined towards Bamtam 18 May 1688, arrived at Batavia coming from Bantam 23 May 1688
Claverblad, small boat, arrived at Batavia coming from Macassar 27 May 1688
Couwerven, ship, arrived coming Bantam to be repaired at Onrust 12 May 1688
Craanvogel, small yacht, mentioned in letters brought by Chinese vessels coming from Soerabaja 11 and 12 May 1688
Drakensteijn, fluyt, destined towards Malacca 18 May 1688, departed towards Malacca 21 June 1688, arrived at Batavia coming from Bantam 30 June 1688
Eemland, yacht, destined towards the trade on Aijmuij 5 May 1688, if there wasn't any trade possible at Aijmuij she was to go towards Macao 18 May 1688, departed towards Aijmuij 27 June 1688
Egelenburg, fluyt, also called small fluyt, destined towards Bengal 18 May 1688, departed Batavia towards Japara 28 May 1688, arrived at Batavia coming via Samarang from Japara 27 June 1688
Egmont, chialoup, arrived at Batavia coming via Japara from Timor 20 June 1688
Gaasperdam, yacht, destined towards Toncquin 28 May 1688
Gideon, fluyt, arrived at Batavia coming via Japara and Cheribon from Macassar 29 May 1688
Groote Visserije, arrived at Batavia coming from Bantam 5 May 1688, destined with Batavian sugar towards Persia 1 June 1688
Hendrik Maurits, ship, arrived at Batavia coming with spices from Banda 29 June 1688
Hollandsen Thuijn, ship arrived at Batavia coming from Cheribon? 3 May 1688, destined towards Indermaijoe 18 May 1688, departed towards Cheribon 28 May 1688
Jambij, small yacht, destined to patrol in Madura Strait 18 May 1688, before departing towards Japara first ordered to patrol in Madura Strait 7 June 1688
Leck, ship, destined via Siam towards Japan 8 May 1688
Maas, ship, destined towards Japara and Rembangh 18 May 1688
Macassar, ship, decided to replace her by the Odijk at Japara 18 May 1688
Meerkat, store vessel, arrived at Batavia coming from Tanjongpoura 16 May 1688
Negombo, yacht, destined towards Malacca 18 May 1688, departed towards Malacca 21 June 1688
Odijk, yacht, destined to transport the second prince of Cheribon 5 May 1688, ordered to replace the Macassar at Japara 18 May 1688, mentioned as used as transport for war prisoners 22 June 1688
Oosterlant, ship, departed Batavia towards Japan 27 June 1688
Oostersouburg, ship, arrived at Batavia coming from Japara with woodwork 9 May 1688, destined towards Japan 18 May 1688
Opmeer, fluyt, also called cat, hull from the fluyt sold for 120 rijksdaalders 22 May 1688, the laid up cat Opmeer sold for 120 realen 18 June 1688
Orangie, small yacht, arrived at Batavia coming via Japara from Timor 20 June 1688
Paliacatta, chialoup, arrived at Bantam via Bantam from Lampon 31 May 1688
Peperthuijn, yacht, destined with 50 European soldiers towards Jambij and Permissang 4 May 1688, departed Batavia towards Jambij and Permissang 5 May 1688,
Pijlswaart, yacht, arrived at Batavia coming from Amboina 2 June 1688
Purmer, yacht, destined towards Coromandel 18 May 1688
Schelvis, pantjalang, arrived at Batavia coming from Cheribon 20 June 1688
Sint Martensdijck, yacht, destined towards the islands of Macao 18 May 1688, destined towards Canton 27 June 1688
Sint Nicolaas, yacht, departed Batavia via Japara towards Soerabaja 18 May 1688
Snoek, pantjalang, mentioned 21 and 27 June 1688
Sumatra, ship, arrived at Batavia coming from Cheribon 1 May 1688
Vlieger, arrived at Batavia coming from Bantam 21 June 1688
Vrijheijt, ship, embarked 24 European soldiers destined towards Cheribon 17 May 1688, destined towards Cheribon with stores valued ƒ 1757:19:02 18 May 1688
Wapen van Tertholen, arrived at Batavia coming from the West Coast of Sumatra 25 May 1688
Waterlant, ship, arrived at Batavia coming from Japara with woodwork 2 May 1688, destined towards Japara, Damak and Rimbang 18 May 1688, destined towards Japara for woodwork 7 June 1688
Waveren, fluyt, arrived at Batavia coming from Cheribon 16 May 1688, destined towards Bengal 18 May 1688
Westbroek, fluyt, arrived at Batavia coming from Bengal 3 June 1688
Wijk op Zee, yacht, arrived at Batavia coming with pepper from Bantam 27 June 1688