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. 2506. 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.
Aep, pantjalang, arrived at Batavia coming from Tanjongpoura 1 May 1690
Casteel van Batavia, chialoup, departed Batavia towards Sunda Strait 22 May 1690, arrived at Batavia coming from the Sunda Strait with the bookholder of the Crap 24 May 1690
Cheribon, chialoup, arrived at Batavia coming from Bantam 3 May 1690, departed Batavia towards Bantam 28 May 1690
Coninck van Bantam, yacht, destined towards Tagal for a cargo of wood 2 Amy 1690, departed Batvai towards Tagal 6 May 1690
Crap, ship, chamber Hoorn, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 104 men 25 May 1690
Duijf, small fluyt, arrived at Batavia coming from the West Coast of Sumatra 8 May 1690
Eemland, yacht, destined from Bengal towards Ceylon and from there to the Netherlands or to return to Batavia 19 May 1690, departed Batavia via the West Coast of Sumatra towards Bengal 23 may 1690
Faem, yacht, destined towards Bengal 15 May 1690, destined from Bengal towards Ceylon and from there to the Netherlands or to return to Batavia 19 May 1690
Montfoort, fluyt, destined via Ceylon towards Bengal 2 May 1690
Schoondijk, ship, mentioned that 50 European soldiers were embarked 12 May 1690, destined via Potno Pedra and Nagapatnam towards Paliacatta 15 May 1690
Sumatra, ship, destined towards Indermaijoe 2 may 1690, departed Batavia towards Cheribon with 800 lb gunpowder 6 May 1690
Vogelstruijs, pantjalang, departed Batavia towards Bantam 19 May 1690, arrived at Batavia coming from Bantam 27 May 1690, departed Batavia towards Bantam 28 May 1690
Vrijheijd, ship, arrived at Batavia coming from Cheribon with a cargo of wood 23 May 1690
Waelstroom, ship, destined via Siam towards Japan 6 May 1690
Westeramstel, fluyt, arrived at Batavia coming via Japara from Rembang with a cargo of wood 31 May 1690
Wijck op Zee, yacht, destined towards Bengal 15 May 1690