Ida Sawyer, the HRW's Central Africa director, said two of the victims were killed outside St. Alphonse church in the Matete district of the capital Kinshasa on Sunday.
Catholic Churches and activists had called for protests after Sunday mass against President Joseph Kabila's refusal to step down.
Georges Kapiamba, a human rights activist, said that nearly 50 people were arrested in Kinshasa.
At the Paroisse Saint Michel in Kinshasa's Bandalungwa district, security forces fired teargas into the church, creating panic.
Pierrot Mwanamputu, a police spokesman, denied that security forces had used live fire during the protests. "We are operating in the daytime. Everyone is watching us. It's not the night."
At the Notre Dame du Congo cathedral in Kinshasa's Lingwala district, where opposition leader Felix Tshisekedi was attending mass, police and soldiers blocked the path of over 100 opposition supporters as they prepared for a march.
At another church in the working-class district of Barumbu, a few dozen police officers used teargas and stun grenades against some 300 churchgoers.
Separately, more than two dozen were detained and three more seriously injured in the southeastern town of Kamina.
The police have banned demonstrations and said all gatherings of more than five people would be dispersed to ensure public order. Across Kinshasa, police and soldiers searched vehicles and checked passengers' identifications.
On Saturday, authorities ordered all internet and SMS services cut until further notice.
Last year, President Kabila committed to holding an election to choose his successor by the end of 2017, an election that has now been delayed until December 2018.
The DRC had one of the most brutal colonial rules before undergoing decades of corrupt dictatorship and back-to-back civil wars that left the mineral-rich country poor and politically unstable.
In 2006, the UN mission helped carry out Congo's first free and fair elections in 46 years, paving the way for Kabila to be elected for a five-year term.
His second term in office ended in 2016. Under the DR Congo's constitution, Kabila is banned from seeking a third term. However, he is authorized to stay in office until his successor is elected but he decided to remain in power. This prompted the UN to urge the Congolese authorities "to respect the fundamental freedoms enshrined in the Congolese Constitution."
The delay in holding an election has flared up violence in the country.