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. 2495. 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, chamber Amsterdam, news of arrival at Cape of Good Hope 28 July 1683, arrived at Batavia coming from the Netherlands 30 July 1683 with 207 men and a cargo valued ƒ 178609 for chamber Amsterdam, ƒ 75670 for chamber Rotterdam and ƒ 81301 for chamber Delft 30 July 1683
Bode, hooker, departed Batavia towards Cheribon 13 July 16893
Bracq, small yacht, arrived at Batavia coming from Intchiassem 13 July 1683, destined towards Palembang 22 July 1683
Burg van Leijden, ship, chamber Zealand, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 288 men and a cargo valued ƒ 202081 28 July 1683
Couwerven, ship, arrived at Batavia coming from Bantam 28 July 1683
Craanvogel, small yacht, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Delfshaven, fluyt, arrived at Batavia coming from Cheribon 5 July 1683
Egmont, chialoup, arrived at Batavia coming from the river Craoang 15 July 1683, departed Batavia towards the river Craoangh 17 July 1683
Gaasperdam, ship, news of arrival at Cape of Good Hope 28 July 1683
Griffioen, chialoup, also called frigate, arrived at Batavia coming from Craoangh 8 July 1683, destined towards Palembang 22 July 1683
Hooger Geest, ship, news of arrival at Cape of Good Hope 28 July 1683
Hoop, small yacht, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Huijs te Cleeff, yacht also called ship, mentioned 1 July 1683, mentioned 6 July 1683
Land van Schouwen, ship, chamber Amsterdam, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 291 men and a cargo valued ƒ 338444:18:08 10 July 1683
Lelij, chialoup, departed Batavia towards the West Coast of Sumatra 14 July 1683
Naardermeer, cat, arrived at Batavia coming from Cheribon and Indermaijoe 14 July 1683
Roemerswaal, ship, mentioned 6 July 1683
Salm, chialoup, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Smith, yacht, departed Batavia towards Bantam 13 July 1683
Snauw, chialoup, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Sumatra, destined via Ternate towards Amboina 21 July 1683
Suijt Bevelant, ship, departed Batavia towards Bantam 13 July 1683, arrived at Batavia coming from Bantam 28 July 1683
Tertholen, ship, destined towards Japan 3 July 1683
Tijger, mentioned as cruising off the river Craoangh, commanded by Jacob Vos 13, 17 and 28 July 1683
Voorhout, small yacht, mentioned 6 July 1683
Waveren, ship, destined towards Japan 3 July 1683
Wester Amstel, ship, news of arrival at Cape of Good Hope 28 July 1683
Africa, ship, chamber Amsterdam, news of arrival at Cape of Good Hope 28 July 1683, arrived at Batavia coming from the Netherlands 30 July 1683 with 207 men and a cargo valued ƒ 178609 for chamber Amsterdam, ƒ 75670 for chamber Rotterdam and ƒ 81301 for chamber Delft 30 July 1683
Bode, hooker, departed Batavia towards Cheribon 13 July 16893
Bracq, small yacht, arrived at Batavia coming from Intchiassem 13 July 1683, destined towards Palembang 22 July 1683
Burg van Leijden, ship, chamber Zealand, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 288 men and a cargo valued ƒ 202081 28 July 1683
Couwerven, ship, arrived at Batavia coming from Bantam 28 July 1683
Craanvogel, small yacht, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Delfshaven, fluyt, arrived at Batavia coming from Cheribon 5 July 1683
Egmont, chialoup, arrived at Batavia coming from the river Craoang 15 July 1683, departed Batavia towards the river Craoangh 17 July 1683
Gaasperdam, ship, news of arrival at Cape of Good Hope 28 July 1683
Griffioen, chialoup, also called frigate, arrived at Batavia coming from Craoangh 8 July 1683, destined towards Palembang 22 July 1683
Hooger Geest, ship, news of arrival at Cape of Good Hope 28 July 1683
Hoop, small yacht, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Huijs te Cleeff, yacht also called ship, mentioned 1 July 1683, mentioned 6 July 1683
Land van Schouwen, ship, chamber Amsterdam, arrived at Batavia coming via Cape of Good Hope from the Netherlands with 291 men and a cargo valued ƒ 338444:18:08 10 July 1683
Lelij, chialoup, departed Batavia towards the West Coast of Sumatra 14 July 1683
Naardermeer, cat, arrived at Batavia coming from Cheribon and Indermaijoe 14 July 1683
Roemerswaal, ship, mentioned 6 July 1683
Salm, chialoup, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Smith, yacht, departed Batavia towards Bantam 13 July 1683
Snauw, chialoup, destined via Bantam towards the so-called Duijsent island for patrolling against pirates 23 July 1683
Sumatra, destined via Ternate towards Amboina 21 July 1683
Suijt Bevelant, ship, departed Batavia towards Bantam 13 July 1683, arrived at Batavia coming from Bantam 28 July 1683
Tertholen, ship, destined towards Japan 3 July 1683
Tijger, mentioned as cruising off the river Craoangh, commanded by Jacob Vos 13, 17 and 28 July 1683
Voorhout, small yacht, mentioned 6 July 1683
Waveren, ship, destined towards Japan 3 July 1683
Wester Amstel, ship, news of arrival at Cape of Good Hope 28 July 1683