The deputy chairman of the opposition Musavat Party, Tofiq Yaqublu, and the chairman of REAL movement, Ilqar Mammadov, were arrested and on February 4 charged with organization of mass disorder.
The charges related to large protests in the town of Ismayilli, 150 kilometers northwest of the capital, Baku, on January 23.
Yaqublu and Mammadov arrived in Ismayilli the next day, calling for acts of civil disobedience.
They face significant fines or up to three years in jail if found guilty.
The information officer at the U.S. Embassy in Baku, Jonas Stewart, told RFE/RL on February 6 that "in all cases related to the events of January 23-24 and other recent protests, we urge the government of Azerbaijan to observe due process of the law and ensure transparency and fairness of the judicial process."
Human Rights Watch has also expressed concern that the two men's arrest may be politically motivated.
"We're concerned that last month's violence will be used as a pretext to silence two outspoken government critics," said Giorgi Gogia, senior South Caucasus researcher at Human Rights Watch.
"The authorities should release Mammadov and Yaqublu from pretrial detention and produce credible evidence that the charges are justified."
Amnesty International has also condemned the arrests, describing the case as having "all the hallmarks of a politically motivated prosecution," according to David Diaz-Jogeix, the rights watchdog's deputy director for Europe and Central Asia.
Meanwhile, Azerbaijan has continued its crackdown against the Ismayilli protesters. Six residents of the village of Hacihasanli in the Ismayilli district have been arrested in connection with last month's mass protests.
Relatives of the six men told RFE/RL on February 6 that they were still in custody. Ismayilli district authorities say they have arrested 14 people.
All have been charged with damaging private property and disobeying police orders.