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, ships, destined towards Cheribon for a cargo of wood 3 March 1701
Baros, chialoup, arrived at Batavia coming from the West coast of Sumatra with a cargo valued ƒ 30.690:17:00 26 March 1701
Casteel Batavia, yacht, decided to sent a large amount of cash towards Bantam and to return with a cargo of pepper 4 March 1701, departed Batavia towards Bantam with a cargo valued ƒ 122.029:01:02 10 March 1701, arrived at Batavia coming from Bantam with a cargo valued ƒ 84.737:12:08 28 March 1701
Crab, chialoup, departed Batavia towards Cheribon 19 March 1701, arrived at Batavia coming from Cheribon 28 March 1701
Dorell, British ship, arrived at Batavia coming from China 1 March 1701, departed Batavia towards England 5 March 1701
Driekroonen, ship, tiding of her arrival at Cape of Good Hope underway towards the Netherlands 24 March 1701
Etershem, fluyt, decided to sent her for a cargo of woodwork towards Tagal 11 March 1701, departed Batvia towards Japara 19 March 1701
Fredericus Quartus, Danish East Indiaman, tiding of her arrival at Cape of Good Hope 24 March 1701
Godfrigt, British ship, due to the fact that she had take some survivors of the Harwits on board became her crew too large and she allowed sailors to leave the ship 1 March 1701
Happij Return, British ship, tiding of her arrival at Cape of Good Hope coming from England 24 March 170
Hartloop, frigate, arrived at Batavia from her cruising for pirates in Banca Strait 7 March 1701
Harwits [Harwich?], British ship, wrecked in China 1 March 1701
Heeren Freguat [Lords’frigate?], British ship, arrived at Batavia coming from Banjer 16 March 1701
Hof van Ilperdam, ship, arrived at Batavia coming from the Netherlands24 March 1701
Houtsnip, chialoup, laid up 29 March 1701
Middelburg, chialoup, arrived at Batavia coming via Palembang from Malacca with a cargo valued ƒ 200:11:05 taken on board at Palembang 20 March 1701
Noordgouw, frigate, tiding of her arrival at Cape of Good Hope coming from Texel 24 March 170
Oostersteijn, ship, tiding of her arrival at Cape of Good Hope underway towards the Netherlands 24 March 1701
Oosthuijsen, fluyt, departed Batavia towards Samarang 26 March 1701
Pampus, yacht, mentioned 1 March 1701, arrived at Batavia from her cruising for pirates in Banca Strait 7 March 1701, destined towards the East coast of Java for a cargo of woodwork 18 March 1701, departed Batavia towards Japara 21 March 1701
Pentsjar, British ship, arrived at Batavia coming from Borneo 8 March 1701, departed Batavia towards England 20 March 1701
Peperthuijn, arrived at Batavia coming from Siam [Thailand] with a cargo belonging to the company valued ƒ 31.622:13:00 and 400 boxes of copper belonging to the crown and some of his servants 7 March 1701
Peter en Paul, frigate, mentioned 2 March 1701
Purmer, yacht, destined towards the East coast of Java for a cargo of woodwork 18 March 1701, departed Batavia towards Tagal 19 March 1701
Santo Francisco, Portuguese chialoup, arrived at Batavia coming from Siam [Thailand] 7 March 1701
Soelen, fluyt, destined towards Japan 22 March 1701
Susanna, small yacht, arrived at Batavia coming via Palembang from Malacca with a cargo valued ƒ 21.655:09:08 taken on board at Palembang and a cargo of white pepper valued ƒ 97:19:08 taken on board at Malacca 20 March 1701
Tonijn, chialoup, departed Batavia towards Tanjongoura 19 March 1701
Trumbal Galeij, British ship, arrived at Batavia coming from China 19 March 1701
Unie, ship, arrived at Batavia coming via Mallabar from Souratta with a cargo valued ƒ 64.238:18:08 8 March 1701, destined towards Ceylon but first to do a voyage towards Cheribon for a cargo of rice and other stores 22 March 1701
Venhuijsen, ship, tiding of her arrival at Cape of Good Hope underway towards the Netherlands 24 March 1701
Zuijd Pool, galliot, arrived at Cape of Good Hope coming from the Netherlands with official papers for Gamron 24 March 1701