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.'s 2496-2497. 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.
Africa, ship, news that she was abandoned by the crew and burnt 300 miles from the coast 27 July 1684
Beurs, yacht, destined towards Japan 12 July 1684
Bombain, yacht, departed Batavia towards Toncquin 12 July 1684
Bovencarspel, fluytship, departed Batavia [towards Japan?] 3 July 1684
Brack, yacht, with all equipment sold for 610 rijksdaalders to the Chinese Tsoa Hin Ko 4 July 1684
Craanvogel, hooker, departed Batavia towards Toncquin 12 July 1684
Delfshaven, fluyt, departed Batavia towards Cherbon, with a cargo valued ƒ 21785:12:06, 29 July 1684
Eemlant, yacht, destined towards Japan 12 July 1684
Egelenburg, fluyt, arrived at Batavia coming from Japara with two new chiampans 15 July 1684
Faam, ship, news of arrival at Cape of Good Hope coming from the Netherlands 27 July 1684
Gecroonde Vreede, ship, laid up due to being incapable 18 July 1684
Hellevoetsluijs, ship, arrived at Batavia coming from Bantam 9 July 1684
Honsholredijk, ship, arrived at Batavia coming via the West Coast of Sumatra from Coromandel 26 July 1684
Jambij, yacht, departed Batavia towards Bengal 29 July 1684
Juffrouw Anna, yacht, hired, destined via Coromandel and Ceylon towards the Netherlands 12 July 1684
Langewijk, ship, news of arrival at Cape of Good Hope coming from the Netherlands 27 July 1684
Macassar, ship, mentioned as being in Sunda Strait 5 July 1684
Nederhorst, yacht, departed Batavia towards Bengal 29 July 1684
Negombo, yacht, departed Batavia towards Bengal 29 July 1684
Oosterblocker, fluyt, arrived at Batavia coming from Cheribon 18 July 1684
Piesang, chialoup, departed Batavia towards Sunda Strait 5 July 1684, arrived at Batavia coming from Sunda Strait 10 July 1684, departed Batavia towards Bantam 29 July 1684
Pijl, yacht, laid up due to being incapable 25 July 1684
Post, ship, news of arrival at Cape of Good Hope coming from the Netherlands 27 July 1684
Roemerswaal, yacht, departed Batavia towards Bantam 18 July 1684
Romeijn, yacht, chamber Amsterdam, hired, arrived at Batavia coming via cape of Good Hope from the Netherlands, cargo valued ƒ 71283:08:00, 131 men, 23 July 1684, destined via Bengal towards the Netherlands 25 July 1684
Rooseboom, chialoup, arrived at Batavia coming via Banda from Sunda Strait 15 July 1684
Schelde, ship, chamber Zealand, arrived at Batavia coming via Cape of Good Hope from the Netherlands, cargo for chamber Zealand valued ƒ 155187:04:10, cargo valued for chamber Rotterdam valued ƒ 73331:11;)9, 231 men, 27 July 1684
Sint Martensdijck, yacht, departed Batavia towards Bengal 29 July 1684
Soestdijck, fluyt, arrived at Batavia coming from Palembang, with a cargo of pepper valued ƒ 40240 30 July 1684
Veluwe, ship, laid up due to being incapable 18 July 1684
Waveren, fluyt, departed Batavia [towards Japan?] 3 July 1684