The Ahmadiyah identify themselves as Muslims, but believe another prophet followed the Prophet Mohammed, who founded Islam. Many mainstream Muslims and hardline groups accuse the sect and other Muslim minorities of apostasy.
A mob of 1,000 people beat to death three Ahmadis in an unprovoked attack in a village in Banten province, west of Jakarta, in 2011 and activists say the group continues to face discrimination.
Indonesia's reputation for tolerance has come under renewed scrutiny since Jakarta Governor Basuki Tjahaja Purnama, a Christian, was sentenced last month to two years in prison for blasphemy in a trial that came after mass Islamist-led rallies and raised religious tensions to the highest in years.
Sixteen people from the village of Manislor in West Java, representing 1,400 members of the sect, told the ombudsman on Tuesday that their lives had been damaged by not having IDs for five years, said Syamsul Alam Agus, executive secretary of One Justice Foundation, a nonprofit organization.
Some were unable to register their marriages, Agus said, adding in one case an Ahmadi was refused treatment at a hospital because of a lack of ID.
According to Agus, in order to obtain ID documents, Ahmadis had to sign a form stating they were Muslims while reading the Shahada, an Islamic creed declaring belief in the oneness of God and Muhammad as God's prophet.
"Not giving an electronic ID card to Manislor's Ahmadiyah followers is not only a violation of human rights, but also breaking the law," Agus said.
Indonesia requires a person to state their religion on official ID cards.
The Kuningan government could not be reached for comment on Wednesday, but in a June 2016 post on its website, the head of the Kuningan regency, Acep Purnama, defended its refusal to hand out identity documents to followers of Ahmadiyah and an animist belief, Sunda Wiwitan.
"We are not discriminating or being intolerant... But this is an issue of principle that has to be resolved together and must be accepted by all Kuningan people. This isn't about majority or minority," he was quoted as saying.
Earlier this month, the government of Depok city near Jakarta sealed off a mosque frequently used by Ahmadis during the Muslim fasting month of Ramadan, according to media reports.
Muslims make up nearly 90 percent of Indonesia's 250 million people but there are sizeable communities of Buddhists, Hindus, Christians and people who adhere to traditional beliefs.
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