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.2519. 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.
Bije, yacht, arrived at Batavia coming from Bengal 15 January 1699
Caauw, small yacht, arrived at Batavia coming from Tonkin 6 January 1699, departed Batavia towards Bantam 28 January 1699
Cadirij, small yacht, laid up 2 January 1699, sold 23 January 1699
Ceram, chialoup, departed Batavia towards Amboina 5 January 1699
Coning van Bantam, yacht, departed Batavia towards Amboina 16 January 1699
Emmenes, fluyt, arrived at Batavia coming from Bengal 6 January 1699
Faam, yacht, arrived at Batavia coming from Ceylon after transporting a cargo from Mocha destined for the Netherlands 19 January 1699
Geelvink, yacht, arrived at Batavia coming from Bengal 22 January 1699
Geregtigheijt, chialoup, departed Batavia towards Bantam 3 January 1699, arrived at Batavia coming from Bantam 12 January 1699
't Huijs te Dieren, fluyt, mentioned to depart soon towards the Netherlands 10 January 1699, departed Batavia towards the Netherlands 22 January 1699
't Huijs te Duijne, small yacht, arrived at Batavia coming from Bengal 8 January 1699
't Huijs te Nieuwburg, fluyt, mentioned to depart soon towards the Netherlands 10 January 1699, departed Batavia towards the Netherlands 22 January 1699
Jerusalem, fluyt, chamber Rotterdam, arrived at Batavia coming from the Netherlands 9 January 1699
Johor, chialoup, departed Batavia via Bima towards Macassar 15 January 1699
Leeuwerk, galliot, departed Batavia towards Timor 3 January 1699
Padang, chialoup, arrived at Batavia coming from the West Coast of Sumatra 20 January 1699
Pampus, yacht, tidings of her arrival at Bengal after a long voyage and all ready thought she was lost 22 January 1699
Pool, frigate, departed Batavia towards Macassar 6 January 1699
Saamslag, yacht, departed Batavia towards Banda 15 January 1699
Schelde, yacht, arrived at Batavia coming from Malacca 30 January 1699
Soldaet, frigate, departed Batavia towards Amboina 16 January 1699
Wijck op Zee, yacht, departed Batavia towards Ternate 16 January 1699
Bije, yacht, arrived at Batavia coming from Bengal 15 January 1699
Caauw, small yacht, arrived at Batavia coming from Tonkin 6 January 1699, departed Batavia towards Bantam 28 January 1699
Cadirij, small yacht, laid up 2 January 1699, sold 23 January 1699
Ceram, chialoup, departed Batavia towards Amboina 5 January 1699
Coning van Bantam, yacht, departed Batavia towards Amboina 16 January 1699
Emmenes, fluyt, arrived at Batavia coming from Bengal 6 January 1699
Faam, yacht, arrived at Batavia coming from Ceylon after transporting a cargo from Mocha destined for the Netherlands 19 January 1699
Geelvink, yacht, arrived at Batavia coming from Bengal 22 January 1699
Geregtigheijt, chialoup, departed Batavia towards Bantam 3 January 1699, arrived at Batavia coming from Bantam 12 January 1699
't Huijs te Dieren, fluyt, mentioned to depart soon towards the Netherlands 10 January 1699, departed Batavia towards the Netherlands 22 January 1699
't Huijs te Duijne, small yacht, arrived at Batavia coming from Bengal 8 January 1699
't Huijs te Nieuwburg, fluyt, mentioned to depart soon towards the Netherlands 10 January 1699, departed Batavia towards the Netherlands 22 January 1699
Jerusalem, fluyt, chamber Rotterdam, arrived at Batavia coming from the Netherlands 9 January 1699
Johor, chialoup, departed Batavia via Bima towards Macassar 15 January 1699
Leeuwerk, galliot, departed Batavia towards Timor 3 January 1699
Padang, chialoup, arrived at Batavia coming from the West Coast of Sumatra 20 January 1699
Pampus, yacht, tidings of her arrival at Bengal after a long voyage and all ready thought she was lost 22 January 1699
Pool, frigate, departed Batavia towards Macassar 6 January 1699
Saamslag, yacht, departed Batavia towards Banda 15 January 1699
Schelde, yacht, arrived at Batavia coming from Malacca 30 January 1699
Soldaet, frigate, departed Batavia towards Amboina 16 January 1699
Wijck op Zee, yacht, departed Batavia towards Ternate 16 January 1699