The track supervisor and his assistant are suspected of using inadequate wiring during works on the line in May, the Investigative Committee said.
They have been questioned and charges are expected to be brought soon, it said in a statement.
A power surge is said to have caused the crash, which injured 162 people.
Wednesday has been officially declared a day of mourning in Moscow.
The two men arrested, named as track supervisor Valery Bashkatov and assistant supervisor Yury Gordov, are suspected of failing to properly monitor work carried out on a track switch mechanism in an underground tunnel.
“The switch mechanism was fixed with ordinary 3-mm wire, which snapped,” the Investigative Committee said.
The Moscow metro, one of the world’s busiest, is a vital transport artery for the city, transporting more than nine million people on weekdays below its traffic-clogged streets.
The train derailed between Slaviansky Boulevard and Park Pobedy (Victory Park) stations in the west of the city.
More than 1,100 people were evacuated.
The packed commuter train was travelling from the north-west of Moscow to the city centre at the time of the crash.
The tunnel where crash happened was built about 10 years ago.
Critics accuse the authorities of spending too much on extending the metro system, and not enough on maintenance.
Park Pobedy is the deepest metro station in Moscow, 84m (275ft) underground, which made the rescue operation particularly hard.
No foreigners were among the injured, the Interfax news agency said.
Militant attacks on Russia’s railways and transport networks have killed dozens of people in the past, but the emergencies ministry said there was no suspicion of such a cause in this case.
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