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.
Aerdenhout, small yacht, destined via Cheribon towards Amboina with a cargo valued ƒ 24,223:04:08 11 January 1701
Boswijk, yacht, laid up 7 January 2011
Carthago, ship, arrived at Batavia coming via Malacca from Palembang with a cargo valued ƒ 57,929:01:00 31 January 1701
Casteel van Batavia, chialoup, departed Batavia 30 January 1701
Coning van Bantam, yacht, laid up 7 January 1701
Crab, fluyt, arrived at Batavia coming from Bengal with a cargo valued ƒ 400,301:17:00 2 January 1701
Donkervliet, ship, departed Batavia towards the Netherlands with a cargo valued ƒ 229,295:10:00 29 January 1701
Eenhoorn, ship, destined via Macassar towards Banda with a cargo valued ƒ 129,031:09:06 11 January 1701
Generale Vreede, departed Batavia towards Amboina with a cargo valued ƒ 157,220:11:08 29 January 1701
Haak, ship, departed Batavia towards the Netherlands with a cargo valued ƒ 182,218:18:08 29 January 1701
Haas, small fluyt, arrived at Batavia coming from Cheribon with a cargo valued ƒ 20,874:04:03 8 January 1701
Hartloop, fluyt, mentioned 8 January 1701
Hoen, galliot, arrived at Batavia coming from Cheribon 21 January 1701
Langewijk, fluyt, departed Batavia towards Bantam for a cargo of pepper with on board a cargo valued ƒ 42,636:01:00 21 January 1701
Madras, British ship, departed Batavia via Bankahoele to England 6 January 1701
Mansoen, British ship, departed Batavia towards Madras 9 January 1701
Pampus, yacht, tiding of her arrival at Sumatra 6 January 1701, still at Sumatra 11 January 1701
Peter en Paul, frigate, destined towards the Netherlands 10 January 1711
Petronella, chialoup, arrived at Batavia coming from Japara 7 January 1701
Pool, frigate, departed Batavia towards the homeward bound fleet 28 January 1701
Schelde, yacht, arrived at Batavia coming from Bantam with a cargo valued ƒ 75,567:14:00 12 January 1701
Santa Anna Santa Maria, Portuguese chialoup, arrived at Batavia coming from Manila 20 January 1701
Theeboom, departed Batavia towards the Netherlands with a cargo valued ƒ 223,634:12:00 29 January 1701
Toskaanse Galeij [Tuscan Galley], British ship, arrived at Batavia coming from China 28 January 1701
Waterman, fluyt, departed Batavia via Amboina towards Banda via a cargo valued ƒ 95,127:17:00 18 January 1701
Wind, small yacht, arrived at Batavia coming from the West Coast of Sumatra 26 January 1701