Speaking at the Basmanny courthouse in Moscow, Anna Fadeeva confirmed Zaur Dadaev and Anzor Gubashev had been charged. However, she did not specify the charges.
Dadaev and Gubashev had been identified as suspects by Federal Security Service director Alexander Bortnikov a day earlier.
Until the three other men were taken to the court yesterday, there had been no official confirmation of other suspects.
Mr Bortnikov gave no details of how the men had been detained or specifics on how they were connected to the killings.
However, state news agencies Tass and RIA Novosti said the pair had been detained in Ingushetia, a republic bordering Chechnya, citing Ingush Security Council chief Albert Barakhoev.
Dadaev had served in a battalion of interior ministry troops in Chechnya, Mr Barakhoev said.
He said Gubashev had worked at a private security company in Moscow.
There was scant information about the identity of the three other suspects. Mr Barakhoev was quoted by RIA Novosti as saying two others had been seized at the same time as Dadaev and Gubashev. But there had been no official announcement of their detention.
Shortly before the court session began yesterday, investigating committee spokesman Vladimir Markin revealed there was a fifth suspect, but gave no details.
Mr Nemtsov’s murder shocked Russia’s already beleaguered and marginalised opposition supporters. Suspicion in the opposition is high that the killing had been ordered by the Kremlin in retaliation for Mr Nemtsov’s criticism of president Vladimir Putin. The 55-year-old had been working on a report about Russian military involvement in the eastern Ukraine conflict.
But Russia’s top investigative body said it was looking into several possible motives, including that he had been killed in an attempt to smear Mr Putin’s image. It also said it was looking into possible connections to Islamic extremism and into Mr Nemtsov’s personal life.
Chechnya, where Dadaev reportedly worked, has had two wars in the past 20 years between Russian forces and separatists increasingly allied with fundamentalist Islam. Although the insurgency died down in Chechnya several years ago, attacks attributed to Islamic militants sporadically occur in nearby regions.
Chechnya’s strongman, Kremlin-backed president Ramzan Kadyrov, has imposed Islam-tinged rule in the area, including the mandatory wearing of headscarves by women. Himself a former rebel, he has been widely accused of rampant human rights, abuses including executions and abductions of opponents.
Many believe Mr Nemtsov’s death in a tightly secured area near the Kremlin would not have been possible without official involvement, and could have been an attempt to scare other government foes. Mr Putin, who has called Mr Nemtsov’s killing a “provocation”, did not comment on the detentions.