Five members of the band Pussy Riot -- wearing brightly colored homemade ski masks and miniskirts -- briefly seized the pulpit of Moscow's Christ the Savior Cathedral in late February to chant "Mother Mary, drive Putin away."
In less then a minute, the women were rounded up by security guards. Two of them were later arrested and face up to seven years in jail on charges of hooliganism.
Putin, who won a third presidential term in a March 4 election, described the performance as "unpleasant for all believers" and expressed hope that it would not be repeated.
The Russian Orthodox Church said the women deserve "fair justice" for the "blasphemous" performance at the cathedral, although thousands of believers signed a petition urging the church to forgive the band.
Moscow City Court spokeswoman Anna Usacheva said Wednesday that Maria Alekhina and Nadezhda Tolokonnikova will remain in custody until a hearing in late April. She said the other performers also will be identified and arrested.
Attorneys for the arrested band members said the two women should be released because they have young children. The women have declared a hunger strike to protest their continued detention, the attorneys said.
The band gained notoriety in January for performing an anti-Putin song on Red Square from a spot used in czarist Russia for announcing government decrees. A video of the performance became an Internet hit.
About 20 Orthodox activists rallied in front of the court and some clashed with supporters of the band.
"You shouldn't bring such behavior into a church," said Orthodox activist Nikita Slepnev. "We don't need dancing prostitutes in our churches."
Although church and state are separate under Russia's constitution, the Russian Orthodox Church has claimed a leading role in setting moral guidelines for society.
It has called for tighter controls on the content of television broadcasts and for the banning of books such as Vladimir Nabokov's "Lolita."
The church has experienced a revival since the collapse of the officially atheist Soviet Union in 1991. Its growing prominence has caused concern among followers of minority faiths and non-religious Russians.