| Date | Age | Event | Bishop | Title | Current Title |
| 18 Apr 2004 | 44.1 | Ordained Bishop | John Philip Saklil | Bishop of Timika |
| 29 Apr 2004 | 56.5 | Appointed | Albert Malcolm Ranjith Patabendige Don | Apostolic Nuncio to Indonesia | Secretary of the Congregation for Divine Worship and the Discipline of the Sacraments |
| 56.5 | Appointed | Albert Malcolm Ranjith Patabendige Don | Apostolic Nuncio to Timor-Leste | Secretary of the Congregation for Divine Worship and the Discipline of the Sacraments |
| 56.5 | Appointed | Albert Malcolm Ranjith Patabendige Don | Titular Archbishop of Umbriatico | Secretary of the Congregation for Divine Worship and the Discipline of the Sacraments |
| 30 Apr 2004 | 75.5 | Retired | Jacobus Duivenvoorde, M.S.C. | Archbishop of Merauke | Archbishop Emeritus |
| 16 Jun 2004 | 53.9 | Succeeded | Franciscus Kopong Kung | Bishop of Larantuka |
| 75.1 | Retired | Darius Nggawa, S.V.D. † | Bishop of Larantuka | Bishop Emeritus |
| 25 Jul 2004 | 44.6 | Ordained Bishop | Nicolaus Adi Seputra, M.S.C. | Archbishop of Merauke |
| 8 Sep 2004 | 68.5 | Appointed | Francesco Canalini | Apostolic Nuncio to Switzerland |
| 68.5 | Appointed | Francesco Canalini | Apostolic Nuncio to Liechtenstein | Apostolic Nuncio to Switzerland |
| 23 Oct 2004 | 73.4 | Resigned | Pablo Puente Buces | Apostolic Nuncio to Great Britain | Apostolic Nuncio Emeritus |
| 1 Apr 2005 | 87.9 | Died | Petrus Malachias van Diepen, O.S.A. † | Bishop Emeritus of Manokwari-Sorong |
| 10 Dec 2005 | 58.1 | Appointed | Albert Malcolm Ranjith Patabendige Don | Secretary of the Congregation for Divine Worship and the Discipline of the Sacraments |
| 14 Dec 2005 | 54.4 | Appointed | Vincentius Sensi Potokota | Bishop of Maumere | Archbishop of Ende |
| 17 Dec 2005 | 67.5 | Appointed | Pietro Sambi | Apostolic Nuncio to United States of America |
| 2 Jan 2006 | 71.0 | Resigned | Julius Riyadi Darmaatmadja, S.J. | Bishop of Indonesia, Military | Cardinal, Archbishop of Jakarta |
| 55.5 | Appointed | Ignatius Suharyo Hardjoatmodjo | Bishop of Indonesia, Military | Archbishop of Semarang |
| 19 Jan 2006 | 74.1 | Died | Alexander Soetandio Djajasiswaja † | Bishop of Bandung |
| 6 Apr 2006 | 60.7 | Died | Longinus Da Cunha † | Archbishop of Ende |
| 13 Apr 2006 | 53.1 | Appointed | Leopoldo Girelli | Titular Archbishop of Capreae | Apostolic Nuncio to Indonesia |
| 53.1 | Appointed | Leopoldo Girelli | Apostolic Nuncio to Indonesia |
| 23 Apr 2006 | 54.8 | Ordained Bishop | Vincentius Sensi Potokota | Bishop of Maumere | Archbishop of Ende |
| 17 Jun 2006 | 53.3 | Ordained Bishop | Leopoldo Girelli | Titular Archbishop of Capreae | Apostolic Nuncio to Indonesia |
| 10 Oct 2006 | 53.6 | Appointed | Leopoldo Girelli | Apostolic Nuncio to Timor-Leste | Apostolic Nuncio to Indonesia |
| 10 Dec 2006 | 88.2 | Died | Salvatore Pappalardo † | Cardinal, Archbishop Emeritus of Palermo, Italy |
| 14 Mar 2007 | 51.9 | Appointed | Ludovikus Simanullang, O.F.M. Cap. | Bishop of Sibolga |
| 3 Apr 2007 | 53.5 | Appointed | Vincentius Sutikno Wisaksono | Bishop of Surabaya |
| 14 Apr 2007 | 55.8 | Appointed | Vincentius Sensi Potokota | Archbishop of Ende |
| 20 May 2007 | 52.1 | Ordained Bishop | Ludovikus Simanullang, O.F.M. Cap. | Bishop of Sibolga |
| 2 Jun 2007 | 78.4 | Retired | Anton Pain Ratu, S.V.D. | Bishop of Atambua | Bishop Emeritus |
| 47.2 | Appointed | Dominikus Saku | Bishop of Atambua |
| 7 Jun 2007 | 55.9 | Installed | Vincentius Sensi Potokota | Archbishop of Ende |
| 29 Jun 2007 | 53.8 | Ordained Bishop | Vincentius Sutikno Wisaksono | Bishop of Surabaya |
| 18 Sep 2007 | 51.1 | Died | Benyamin Yosef Bria † | Bishop of Denpasar |
| 21 Sep 2007 | 47.5 | Ordained Bishop | Dominikus Saku | Bishop of Atambua |
| 9 Jan 2008 | 78.7 | Died | Darius Nggawa, S.V.D. † | Bishop Emeritus of Larantuka |
| 17 Jan 2008 | 86.5 | Died | Vincenzo Maria Farano † | Archbishop Emeritus of Gaeta, Italy |
| 19 Jan 2008 | 66.3 | Appointed | Girulfus Kherubim Pareira, S.V.D. | Bishop of Maumere |
| 25 Apr 2008 | 66.6 | Installed | Girulfus Kherubim Pareira, S.V.D. | Bishop of Maumere |