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. 2521. 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.
Assendelft. arrived at Batavia coming from Ceylon [Sri Lanka] with a cargo valued ƒ 266,570:15:00 , was not sent to the Netherlands due to lacking enough pepper 13 February 2011
Bellasoor, chialoup, departed Batavia towards Macassar with gifts valued ƒ 137:05:00 10 February 1701
Borneo, British ship, arrived at Batavia coming from England 14 February 1701
Boswijck, yacht, hull sold, 1 February 1701
Casteel Batavia, yacht, arrived at Batavia coming from Souratta with a cargo valued ƒ 368,130:19:00 13 February 1701
Casteel Batavia, chialoup, arrived at Bavavia coming from the Sunda Strait 8 February 8 February 1701
Conink van Bantam, yacht, hull sold, 1 February 1701
Crab, fluyt, destined towards Ternate 1 February 1701, departed Batavia towards Ternate with a cargo valued ƒ 122,465:06:00 10 February 1701
Etershem, fluyt, arrived at Batavia coming from Bengal with a cargo valued ƒ 395,627:07:08 19 February 1701
Faam, yacht, mentioned 23 February 1701
Langewijk, fluyt, arrived at Batavia coming from Bantam 11 February 1701
Lastdrager, chialoup, tiding of her being attacked 13 February 1701
Mackesfiel Galeij, British ship, arrived at Batavia coming from Nimpho 1 February 1701, departed Batavia towards England 5 February 1701
Nierop, fluyt, destined towards Ternate, 5 February 1701
Oosthuijsen, fluyt, arrived at Batavia coming from Siam [Thailand] with a cargo valued ƒ 41,470:12:08 14 February 1701
Peter en Paul, frigate, on board was a cargo valued ƒ 80,000 destined for the Netherlands 1 February 2011, departed Batavia towards the Netherlands for the Chamber Zealand with a cargo valued ƒ 88,250:00:00 17 February 1701
Petronella, chialoup, departed Batavia towards Japara 9 February 1701
Pool, frigate, arrived at Batavia coming back from the homeward bound fleet 5 February 1701
Pruijm, galliot, departed Batavia towards Japara with a cargo valued ƒ 2,812:04:08 and from there to Soerabaja 9 February 1701
Saamslag, yacht, destined towards Banda with a cargo valued ƒ 47,034:00:08 8 February 1701
Schulp, fluyt, arrived at Batavia coming from Bengal with a cargo valued ƒ 187,536:13:08 12 February 1701
Snoeper, galliot, laid up 4 February 1701
Soldaat, chialoup, tiding of her being wrecked near Souratta 14 February 1701
Toscaanse Galeij, British ship, departed Batavia towards England 6 February 2011
Wijk op Zee, ship, tiding of her being wrecked near Souratta 14 February 1701
Wint, frigate, destined towards Ternate 1 February 1701, departed Batavia via Japara towards Timor with a cargo valued ƒ 9,519:03:08 19 February 1701
Zoelen/Soelen, fluyt(-ship), arrived at Batavia coming via Mallabar from Souratta with a cargo valued 178,438:07:08 23 February 1701