The military have visited the Ahmadiyah, who unlike mainstream Muslims do not believe Mohammed was the last prophet, asking some members to sign statements renouncing their faith, Amnesty said citing local rights groups.
"The Ahmadiyah community is facing increasing restrictions, intimidation and attacks because of their beliefs," according to the group's Indonesia and East Timor campaigner Josef Roy Benedict.
Indonesian human rights group Imparsial said it had recorded 56 cases in West Java province in which soldiers allegedly forced Ahmadiyah followers to convert to mainstream Islam.
Soldiers have entered mosques, gathered followers of the sect and "forced them to repent and convert to Islam", the group said.
The government denied forced conversions had occurred, saying military actions were taken to protect the sect from violence at the hands of Muslim fanatics.
Amateur video emerged in February capturing an extremist mob armed with machetes, sticks and rocks attacking Ahmadiyah followers, leaving three dead and sparking international outcry.
"Since then at least four provinces in Indonesia -- South Sulawesi, West and East Java and Banten -- have issued new regional regulations restricting Ahmadiyah activities," Benedict said in a statement.
The restrictions include banning the sect from distributing pamphlets, putting signs in front of their offices and places of worship or wearing anything indicating that they are Ahmadiyah members, Amnesty said.
The rights group called on the authorities "to conduct prompt, independent and impartial investigations" into all reports of intimidation and to bring the perpetrators to justice.
Ahmadiyah have been subject to abuse and persecution since 2008 when curbs were placed on them at the insistence of mainstream Muslims.
Human Rights Watch has condemned violence against them and urged President Susilo Bambang Yudhoyono to sack his religious affairs minister for discrimination and to lift the ban on Ahmadiyah practising in public.
Indonesia's constitution guarantees freedom of religion but rights groups say violence against minorities including Christians and Ahmadis has been escalating since 2008.
There have been cases of Christians being beaten and churches attacked.
