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.
Assendelft, ship, destined towards Ceylon [Sri Lanka] 24 May 170
Bellesoor, chialoup, arrived at Batavia coming from Macassar 2 May 1701, departed Batavia towards Bengal 9 May 1701
Brandenburg, ship, chamber Amsterdam, arrived at Batavia coming from the Netherlands with a cargo valued ƒ 348.821:00 7 May 1701
Carthago, ship, destined to the East Coast of Java 13 May 1701, departed Batavia towards Japara 25 May 1701
Chere Galeij, British ship, arrived at Batavia for victuals while underway to China 12 May 1700, mentioned as delivering two letters coming from Cape of Good Hope 13 May 1701
Daskwood, English ship, arrived at Batavia coming from England 6 May 700
Dieren, fluyt, departed Batavia via the West Coast of Sumatra with a cargo valued ƒ 91.719:12:00 and from there towards Bengal with a cargo valued ƒ 259.174:13:12 3 May 1701
Ellemeet, ship, tiding of her arrival from Bengal [in Sunda Strait?] 9 May 1701, arrived at Batavia coming from Bengal with a cargo valued ƒ 406.248:11:08 12 May 1700
Haas/Haes, small fluyt, departed Batavia towards Bengal with a cargo valued ƒ 254.226:04:08 8 May 1701
Hartloop, yacht, departed Batavia towards Bengal with a cargo valued ƒ 22.714:10:00 8 May 1701
Hof van Ilpendam, ship, destined towards Persia [Iran] 10 May 1701
Huijs te Duijnen, ship, destined towards Ceylon p[Sri Lanka] 24 May 170
Huijs te Loo, departed Batavia towards Coromandel with a cargo valued ƒ 539.894:16:00 8 May 1701
Itershem, ship, destined to the East Coast of Java 13 May 1701
Langewijk, fluyt, departed Batavia towards Tagal with a cargo of woodwork 6 May 1701
Nederland, ship, tiding of her arrival [in Sunda Strait?] from Persia [Iran] 17 May 1701, arrived at Batvia coming via Ceylon [Sri Lanka] from Persia [Iran]with a cargo valued ƒ 135.184:11:00 18 May 1701
Nigtevegt, ship, chamber Amsterdam, tiding of her arrival from the Netherlands 10 May 1701, arrived at Batavia with a cargo valued ƒ 418.546:01:00 14 May 1701
Pool, frigate, departed with sailors and stores towards the Vrijburg for assistance 9 May 1701, returned from Sunda Strait 13 May 1701, destined with the barge of the water fiscal to the islands to search for unknown ship 24 May 1701
Oosthuijsen, fluyt, arrived at Batavia coming via Tagal from Samarang with a cargo valued ƒ 8.006:12:00 21 May 1701
Schelde, ship, destined to the East Coast of Java 13 May 1701, departed Batavia towards Japara 17 May 1701
Soelen, fluyt, tiding o the fire on board while at Batavia 13 May 1701
Tamboer, yacht, departed Batavia towards Bantam with a cargo valued ƒ 69.974:09:08 7 May 1701, arrived at Batavia coming from Bantam with a cargo valued ƒ 16.015:10:00 16 May 1701, destined towards Coromandel to transport fiscal Hendrik Becker 20 May 1701, departed Batavia towards Coromandel with a cargo valued ƒ 221.034:19:00 31 May 1701
Unie, ship, arrived at Batavia coming from Cheribon with a cargo valued ƒ 1.767:15:00 12 May 1700
Vrijburgh, ship, advice letter from Bantam dealing with the condition of the ship coming from Ceylon [Sri Lanka] 8 May 1701, mentioned as being in Sunda Strait 12 May 1701, arrived at Batavia with a cargo valued ƒ 62.233:03:00 14 May 1701
Assendelft, ship, destined towards Ceylon [Sri Lanka] 24 May 170
Bellesoor, chialoup, arrived at Batavia coming from Macassar 2 May 1701, departed Batavia towards Bengal 9 May 1701
Brandenburg, ship, chamber Amsterdam, arrived at Batavia coming from the Netherlands with a cargo valued ƒ 348.821:00 7 May 1701
Carthago, ship, destined to the East Coast of Java 13 May 1701, departed Batavia towards Japara 25 May 1701
Chere Galeij, British ship, arrived at Batavia for victuals while underway to China 12 May 1700, mentioned as delivering two letters coming from Cape of Good Hope 13 May 1701
Daskwood, English ship, arrived at Batavia coming from England 6 May 700
Dieren, fluyt, departed Batavia via the West Coast of Sumatra with a cargo valued ƒ 91.719:12:00 and from there towards Bengal with a cargo valued ƒ 259.174:13:12 3 May 1701
Ellemeet, ship, tiding of her arrival from Bengal [in Sunda Strait?] 9 May 1701, arrived at Batavia coming from Bengal with a cargo valued ƒ 406.248:11:08 12 May 1700
Haas/Haes, small fluyt, departed Batavia towards Bengal with a cargo valued ƒ 254.226:04:08 8 May 1701
Hartloop, yacht, departed Batavia towards Bengal with a cargo valued ƒ 22.714:10:00 8 May 1701
Hof van Ilpendam, ship, destined towards Persia [Iran] 10 May 1701
Huijs te Duijnen, ship, destined towards Ceylon p[Sri Lanka] 24 May 170
Huijs te Loo, departed Batavia towards Coromandel with a cargo valued ƒ 539.894:16:00 8 May 1701
Itershem, ship, destined to the East Coast of Java 13 May 1701
Langewijk, fluyt, departed Batavia towards Tagal with a cargo of woodwork 6 May 1701
Nederland, ship, tiding of her arrival [in Sunda Strait?] from Persia [Iran] 17 May 1701, arrived at Batvia coming via Ceylon [Sri Lanka] from Persia [Iran]with a cargo valued ƒ 135.184:11:00 18 May 1701
Nigtevegt, ship, chamber Amsterdam, tiding of her arrival from the Netherlands 10 May 1701, arrived at Batavia with a cargo valued ƒ 418.546:01:00 14 May 1701
Pool, frigate, departed with sailors and stores towards the Vrijburg for assistance 9 May 1701, returned from Sunda Strait 13 May 1701, destined with the barge of the water fiscal to the islands to search for unknown ship 24 May 1701
Oosthuijsen, fluyt, arrived at Batavia coming via Tagal from Samarang with a cargo valued ƒ 8.006:12:00 21 May 1701
Schelde, ship, destined to the East Coast of Java 13 May 1701, departed Batavia towards Japara 17 May 1701
Soelen, fluyt, tiding o the fire on board while at Batavia 13 May 1701
Tamboer, yacht, departed Batavia towards Bantam with a cargo valued ƒ 69.974:09:08 7 May 1701, arrived at Batavia coming from Bantam with a cargo valued ƒ 16.015:10:00 16 May 1701, destined towards Coromandel to transport fiscal Hendrik Becker 20 May 1701, departed Batavia towards Coromandel with a cargo valued ƒ 221.034:19:00 31 May 1701
Unie, ship, arrived at Batavia coming from Cheribon with a cargo valued ƒ 1.767:15:00 12 May 1700
Vrijburgh, ship, advice letter from Bantam dealing with the condition of the ship coming from Ceylon [Sri Lanka] 8 May 1701, mentioned as being in Sunda Strait 12 May 1701, arrived at Batavia with a cargo valued ƒ 62.233:03:00 14 May 1701