Lawyers calling themselves the "religious freedom defence team" have asked the Supreme Court to review the decree, which they say obstructs religious freedoms.
Abdul Manan, who handles the registration of appeals in Indonesia's Supreme Court, said: "They want to dispute that decree.
"They think it is at odds with parts of the constitution on religion."
Applicant Saor Siagian told the Jakarta Post newspaper that his team represents church groups and the Ahmadiyah Islamic sect.
The Indonesian Ulema Council, which groups Islamic clerics from across the country, has also expressed reservations over the decree but has stopped short of challenging it.
The country's religious affairs and interior ministers last week issued the decree, establishing places of worship, to replace an old and somewhat vague regulation.
Church groups have already said Christians in Indonesia feel increasingly uneasy, especially after some Islamists forced several unlicensed churches to shut down in recent months.
The new decree stipulates that any attempt to set up a house of worship must take into account the religious composition of the district where it is expected to stand.
If the authorities find a request fits the composition, applicants need to show at least 90 people in the area will use the facility and that at least 60 other residents from other religions approve of having it in their neighbourhood.
Besides sealing several churches across Indonesia, some Islamists have also damaged mosques and other facilities belonging to the Ahmadiyah group, which views itself as Muslim but which many brand as heretical.
Around 85% of Indonesia's 220 million people are Muslims, most of them moderates who tolerate other beliefs.