阿赫邁底亞派穆斯林最早傳入印尼是在1925年夏天（大約是在印尼獨立革命前20年），由這個派別的傳教士拉赫馬特·阿里 (Rahmat Ali) 進入蘇門答臘島，在亞齊的塔帕克團（英語：Tapaktuan）開始活動，初期有13名信眾 。[50]這個教派在印尼的宗教發展中曾發揮過影響力，但在現代卻為其他伊斯蘭教機構所不容，甚至激進穆斯林團體會對這個派別採取暴力行為。[50]估計阿赫邁底亞派組織（印尼阿赫邁底亞社團（印尼語：Jamaah Muslim Ahmadiyah Indonesia）(JMAI) 中有400,000名追隨者，相當於印尼穆斯林人口的0.2%，[7]分佈在全國542個分支組織；但印尼宗教事務部（英語：Ministry of Religious Affairs (Indonesia)）估計，這個教派的跟隨者僅約有80,000名，與獨立人士估計不同。[50]印尼另有一個阿赫邁底亞派的分離主義團體 - 拉合爾阿赫邁底亞伊斯蘭傳播運動（Lahore Ahmadiyya Movement for the Propagation of Islam），在印尼被稱為 印尼語：Gerakan Ahmadiyah-Lahore Indonesia (GAI)，自1924年以來即存在於爪哇，到1980年代只有708名跟隨着。[50]
天主教在14世紀和15世紀，因葡萄牙人到印尼群島做香料貿易而傳入當地。其中許多葡萄牙人的目標就是傳播天主教，首先在1534年從摩鹿加群島開始。傳教先驅聖方濟·沙勿略在1546年至1547年間遍訪群島中各島嶼，為數千名當地人施洗。在VOC統治印尼的時期，天主教受到禁止，天主教徒的數量顯著下降。荷蘭人對天主教的敵意有其歷史上的原因，荷蘭人信仰新教，他們經過八十年戰爭最終從信仰天主教的宗主國西班牙取得獨立。VOC加大力度在佛洛勒斯島和帝汶東部施加限制，導致天主教徒數目很顯著的減少。天主教神父受到監禁或處以刑罰，並由荷蘭派來新教神職人員取代。在17世紀，揚·彼得斯佐恩·庫恩擔任荷屬東印度總督期間，有位天主教神父因為在獄中舉行彌撒（英語：Mass in the Catholic Church）而遭到處決。VOC在18世紀末破產後，荷蘭天主教於1800年左右再度合法化，此後荷蘭天主教神職人員一直主導在印尼的傳播事務，直到印尼獨立為止。[52][59]在16世紀的弗洛勒斯島上，曾建有一拉蘭圖卡王國（英語：Kingdom of Larantuka），是東南亞唯一由原住民所建立的天主教王國，第一位國王名叫洛倫佐（Lorenzo）。[60]
截至2018年，印尼人中天主教徒的佔比為3.12%，數目接近新教徒佔比（7.6%）的一半。[62]信徒大多居住在西加里曼丹省、巴布亞省和東努沙登加拉省。弗洛勒斯島和西帝汶島所在的東努沙登加拉省是印尼唯一天主教徒佔多數的省份（約佔總人口的54.14%）。在爪哇島，天主教除爪哇族外，也傳播到印尼華人。[52][63]在今天的佛洛勒斯島，仍然在接近復活節時會舉辦天主教傳統慶典，當地人稱之為聖週（印尼語：Semana Santa）。儀式包括遊行隊伍將耶穌和聖母瑪利亞（當地分別稱為印尼語：Tuan Ana和印尼語：Tuan Ma）的雕像帶到當地海灘，然後前往天主教拉蘭圖卡教區的聖母玫瑰主教座堂（Cathedral of the Queen of the Rosary）。[64]
印尼的印度教具有與其他地區不同的基調。[68][69]印尼把印度教稱為Agama Hindu Dharma（Agama為宗教之義，Dharma為梵語，有哲學上的「法」之義），也採行種姓制度。[70]也把南島民族的信仰元素如崇敬香、神祇、自然神靈和已故祖先融入。並透過印尼哇揚皮影偶戲和舞蹈把印度教的宗教史詩《摩訶婆羅多》和《羅摩衍那》情節演出。在印尼的各派印度教信仰者都有許多共同信仰，印度教主要的5個基本信仰（稱為Panca Srada），包括對一位全能上帝（梵，宇宙的超越本體和終極實在）的信仰，對靈魂和無數地方和祖先神靈和業力的信仰（對互惠行為法則的信仰，而非對重生和轉世的信仰）。此外，印尼印度教更注重藝術和儀式，而非宗教經典、法律和信仰。[68][71]在爪哇島的許多地區，印度教和伊斯蘭教相互間有巨大影響，是導致阿邦甘（英語：Abangan）（保留當地信仰的爪哇伊斯蘭教徒，也稱為「名義上的」穆斯林）和科賈文信仰傳統發生的部分原因。[72]
在蘇卡諾總統於1960年代中期卸任之後，印尼建國五原則（Pancasila）被重申為印尼的官方宗教政策，而此政策只承認一神論。[78]結果是Perbuddhi（印尼佛教組織（Indonesian Buddhists Organisation））創始人體正老和尚（英語：Ashin Jinarakkhita）（印尼出生華人後裔，俗名Tee Boan-an[79]戴滿安）提出佛教有一至尊之神，即成佛種子（英語：Sanghyang Adi Buddha）（印尼語：Sanghyang Adi Buddha）。他還以古爪哇語（英語：Kawi）中撰寫的佛教經典相關歷史以及婆羅浮屠寺廟來支持其立論。[80]
根據新加坡作者與政治家李炯才的看法，Kejawèn沒特定的先知、[91]聖書，[91]也沒有獨特的宗教節日和儀式；這種信仰更多地與每個追隨者內化的超驗視野和信仰，及他們與他人和至高無上神靈的關係有關。因此這些信仰者可在身分證中註明為為6種官方認可的任何一種，但仍依循Kejawèn信仰和生活方式。這種組織鬆散的思想和信仰潮流在1945年的憲法中有合法地位，並在1973年被承認為尊崇一位至高無上的上帝信仰（印尼語：Kepercayaan kepada Tuhan Yang Maha Esa），在某種程度等同取得合法宗教的地位。前總統蘇哈托即自詡為這種信仰的擁護者。[92]
修菩達由穆罕默德·蘇布·蘇墨哈迪維多多（英語：Muhammad Subuh Sumohadiwidjojo）在1920年代創立。 而修菩達這個名字在1940年代後期，當團體經合法注冊後才開始使用。修菩達運動的基礎是倡導修行，通常被稱為靈性修行（英語：latihan）（印尼語：latihan kejiwaan），蘇墨哈迪維多多將其稱為「上帝的力量（the Power of God）」或「偉大的生命力量（the Great Life Force）」的指導。 蘇墨哈迪維多多的目標是依循上帝的旨意達到完美的品格。[94]只有激情、心思和意念與內心的感覺能夠分開時，才能接觸到無處不在的「偉大的生命力量」。[95][96][97]
錫克教徒於1870年代開始移民到印尼（商人，及擔任警衛者）。蘇門答臘島和爪哇島有幾所謁師所和學校，例如有一處建於棉蘭（1911年）。印尼錫克教最高委員會（Supreme Council for the Sikh Religion in Indonesia）在2015年成立。[112]印尼的錫克教信徒約有7,000人（另稱介於10,000至15,000人之間[7]），由於這個宗教並未得到政府正式承認，導致信徒在身分證上註明自己為印度教徒。[113]
印尼政府透過提出宗教間合作計劃，努力緩和緊張局勢。印尼外交部與印尼最著名的伊斯蘭組織伊斯蘭教士聯合會共同舉行國際伊斯蘭學者會議（International Conference of Islamic Scholars），以倡導伊斯蘭溫和主義（英語：Moderation in Islam）（wasat ），據信可因此緩解印尼國內的緊張局勢。[127]「宗教間合作對話：社區建設與和諧」會議於2004年12月6日舉行。東盟國家、澳大利亞、東帝汶、新西蘭和巴布亞新幾內亞均派代表參加這次會議，以討論不同宗教團體之間的合作，盡量減少印尼宗教間的衝突。[127]
Statistik Umat Menurut Agama di Indonesia. Kementerian Agama Republik Indonesia. 2018-05-15 [2020-11-15]. （原始內容存檔於2020-09-03） （印度尼西亞語）. Muslim 231 Million (86.7), Christian 20.45 Million (7.6), Catholic 8.43 million (3.12), Hindu 4.65 million (1.74), Buddhist 2.03 million (0.77), Confucianism 76.630 (0.03), Others/Traditional faiths 126.51 (0.04), Total 266.5 Million
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Penduduk Menurut Wilayah dan Agama yang Dianut [Population by Region and Religion]. Jakarta, Indonesia: Badan Pusat Statistik. 15 May 2010 [20 October 2011]. （原始內容存檔於2018-12-24） （印度尼西亞語）. Religion is belief in Almighty God that must be possessed by every human being. Religion can be divided into Muslim, Christian,, Hindu, Buddhist, Hu Khong Chu, and Other Religion. Muslim 207176162 (87.20%), Christian 16528513 (7), Catholic 6907873 (3), Hindu 4012116 (1.69), Buddhist 1703254 (0.74), Confucianism 71.999 (0.05), Other 112.792 (0.04), Total 237.641.326
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Indonesia: Religious Freedoms Report 2010 （頁面存檔備份，存於互聯網檔案館）, US State Department (2011), Quote: "The Ministry of Religious Affairs estimates that 10 million Hindus live in the country and account for approximately 90 percent of the population in Bali. Hindu minorities also reside in Central and East Kalimantan, the city of Medan (North Sumatra), South and Central Sulawesi, and Lombok (West Nusa Tenggara). Hindu groups such as Hare Krishna and followers of the Indian spiritual leader Sai Baba are present in small numbers. Some indigenous religious groups, including the "Naurus" on Seram Island in Maluku Province, incorporate Hindu and animist beliefs, and many have also adopted some Protestant teachings."
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C.I.C.R.E.D. cites SUSENAS TAHAP KEEMPAT – Sifat Demografi Penduduk Indonesia [National Survey of Social and Economic Fourth Round – Demographic Characteristics of the Population]. Jakarta: Biro Pusat Statistik (Central Bureau of Statistics). 1969. for Table III.10 of "The Population of Indonesia, 1974 World Population Year", p. 31. However, due to inaccessibility of the data source for verification and data collection proximity to census year 1971, referenced 1969 data is not included in this article's table. The Population of Indonesia, 1974 World Population Year(PDF). C.I.C.R.E.D. 2. Jakarta: Lembaga Demografi (Demographic Institute), Universitas Indonesia. 1973: 31–32 [2018-01-18]. LCCN 77366078. OCLC 3362457. OL 4602999M. （原始內容存檔(PDF)於2016-10-21）. The statistical data on religion show that Islam has the highest percentage of adherents with about 87.1 per cent of the population of Indonesia (National Socio Economic Survey, 1969). The second biggest religion in Indonesia is Protestant (5.2%), while Catholic is the third (2.5%). The rest are Hindu (2.0%) and Buddhist (1.1%) and other religions which are not included in the above classification.
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The 1990 census recorded 87.21% Muslims, 6.04% Protestants, 3.58% Catholics, 1.83% Hindus, 1.03% Buddhists and 0.31% as "Others". Population of Indonesia: Results of the 1990 Population (Jakarta: Biro Pusat Statistik, 1992), p. 24, as cited by
Indonesia. The World Factbook. Washington, D.C.: U.S. Central Intelligence Agency. People and Society. 2011-10-18 [2011-11-08]. ISSN 1553-8133. （原始內容存檔於2021-04-13）. Muslim 86.1%, Protestant 5.7%, Roman Catholic 3%, Hindu 1.8%, other or unspecified 3.4% (2000 census)
In 1979, Soeharto retracted official recognition of Confucianism. Hence Confucianism appears in the 1971 census data, but not in 1980 or 1990. In 2000, Indonesia decided to separately categorise Confucianism only during the enumeration process, but did not actually list this option on the printed form. This is not listed as a separate category in the U.N. data. Utomo, Ariane J. Indonesian Census 2000: Tables and Reports for AusAID Explanatory Notes(PDF) (報告). The Australian National University: 7. March 2003. （原始內容(PDF)存檔於2012-04-25）. The six categories for religion were Islam, Catholicism, Protestant, Hinduism, Buddhism, and Other. The decision to have a separate category for Confucianism (Kong Hu Cu) occurred during the enumeration process itself, hence it was not printed in the actual form of the L1. The data on the number of Confucians is only available for certain provinces. However, the number seems much smaller than expected due to the abrupt process of including it in the questionnaire.
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