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.
Berkenrode, fluyt, departed Batavia towards via Ceylon towards Bengal 21 July 1699
Cattendijk, ship, chamber Zealand, arrived at Batavia coming from the Netherlands 1 July 1699
Erinnesteijn, ship, destined in stead of the Zion towards Ceylon 16 July 1699
Gent, ship, chamber Amsterdam, arrived at Batavia coming from the Netherlands 29 July 1699
Handboogh, fluyt, tiding of her arrival in Sunda Strait coming from Bengal 30 July 1699
Hartloper, frigate, destined towards Souratta 20 July 1699
Java, ship, departed Batavia towards Tagal for a cargo of woodwork 16 July 1699, arrived at Batavia coming from Tagal without any results 28 July 1699
Landswelvaren, ship, tiding of her arrival in Sunda Strait coming from the Netherlands 29 July 1699
Macklesfliet, British ship, arrived at Batavia coming from England 28 July 1699
Meerkat, vessel, arrived at Batavia coming from Tanjongpoura 5 July 1699
Nierop, fluyt, departed Batavia towards Bantam for a cargo of pepper 11 July 1699, arrived at Batavia coming from Bantam with a cargo of pepper 21 July 1699
Nieuwlant, ship, tiding that her damage caused to extreme worse weather couldn't be repaired from Ceylon at Cape of Good Hope 28 July 1699
Nigtevegt, departed Batavia towards Tagal for a cargo of bams 24 Huly 1699
Oostvoorn, small yacht, destined via Palembang towards Malacca 3 July 1699
Pampus, yacht, departed Batavia towards Chormandel 7 July 1699
Peperthuijn, yacht, departed Batavia towards Succadana with a cargo of rice and salt for the military force 22 July 1699
Purmer, yacht, departed Batavia towards Japara for a cargo of woodwork 11 July 1699
Saamslag, yacht, destined via Ceylon towards Bengal 25 July 1699
Soldaat, frigate, arrived at Batavia coming via Samarang from Japra 15 July 1699, destined towards Souratta and Persia 16 July 1699
Venhuijsen, fluyt, departed Batavia towards Japan 6 July 1699
Voorschoten, fluyt, tiding of her arrival in Sunda Strait 13 July 1699, arrived at Batavia coming from Souratta 18 July 1699
Waalstroom, tiding of her missing from Ceylon at Cape of Good Hope due to extreme worse weather 28 July 1699
Wijck op Zee, yacht, arrived at Batavia coming via Amboina from Ternate 21 July 1699
