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.2518. 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.
Advento, British small ship, private owned, tidings of her taken over by her own crew 19 November 1698, tidings that her captain and others left for Bencul 26 November 1698
America, British ship, arrived at Batavia coming from Borneo 20 November 1698
Andromeda, yacht, arrived at Batavia coming from the West Coast of Sumatra 26 November 1698
Bekesteijn, yacht, arrived at Batavia coming from Bengal 28 November 1698
Cadirij, small yacht, arrived at Batavia coming via Japara from Surabaya 6 November 1698
Coning van Bantam, yacht, arrived at Batavia coming from Palembang 27 November 1698
Driebergen, fluyt, chamber Delft, arrived at Batavia coming from the Netherlands 22 November 1698, destined towards the Netherlands 25 November 1698
Eemland, yacht, departed Batavia with the Schelde towards Malacca with stores for that factory and in that area 7 November 1698
Fortuijn, small yacht, arrived at Batavia coming via Japara from Surabaya 6 November 1698
Geregtigheijd, chialoup, arrived at Batavia coming with the Snobber from Malacca 23 November 1698
Goa, chialoup, arrived at Batavia coming from Macassar with a cargo of green 'cadjangen' 11 November 1698
't Huijs te Loo, ship, chamber Amsterdam, arrived at Batavia coming from the Netherlands 6 November 1698
't Huijs te Nieuwbrug, ship, tidings of her arrival in Sunda Strait coming from the Netherlands 26 November 1698
Leeuwerk, galliot, arrived at Batavia coming from Bantam with a cargo of white pepper 1 November 1698
London Freguat, British ship, according to tidings visited she Samarang, she recently left Batavia towards Banjer 6 November 1698
Mackereel, pantjalang, departed Batavia with the Vogelstruijs towards Tanjongpoura where 22 slaves from Celebes were waiting for transport 24 November 1698
Palembang, fluyt, arrived at Batavia coming from Bantam with a cargo of pepper and 'harpuis' 29 November 1698
Meerkat, pantjalang, arrived at Batavia coming from Tanjongpoura 13 November 1698
Pampus, yacht, mentioned [as being at Chettigam?] 26 November 1698
Peperthuijn, yacht, departed Batavia towards Palembang 21 November 1698
Pool, galliot, arrived at Batavia coming from Bengal 26 November 1698
Schaapherder, arrived at Batavia coming from Coromandel 29 November 1698
Schelde, yacht, departed Batavia with the Eemland towards Malacca with stores for that factory and in that area 7 November 1698
Snobber, galliot, arrived at Batavia coming with the Geregtigheijd from Malacca 23 November 1698
Soldaat, frigate, departed Batavia towards Bantam for a cargo of pepper 13 November 1698, arrived at Batavia coming from Bantam with a cargo of pepper 19 November 1698
Susanna, yacht, tidings of her loss in Chettigam 26 November 1698
Vogelstruijs, pantjalang, departed Batavia with the Mackereel towards Tanjongpoura where 22 slaves from Celebes were waiting for transport 24 November 1698
Walenburg, ship, arrived at Batavia coming from Japara with a cargo of woodwork 9 November 1698, departed Batavia towards Bantam for a cargo of pepper 18 November 1698
Zaamslag, yacht, arrived at Batavia coming from Bengal 28 November 1698
Zallant, ship, arrived at Batavia coming from Cheribon 22 November 1698