The explosion occurred at around 4:20 a.m. (01:20 GMT) and was caused by a homemade explosive device left near tracks between the Buryulevo-Tovarnaya and Bulatnikovo stations. No one was injured. The blast had a force of around 1.5 kg of TNT equivalent.
One of the detained men is a Moscow resident, and the other two live in the surrounding region, the source told RIA Novosti.
"Investigators have evidence pointing to their direct involvement in this explosion," he said.
During checks, investigators found traces of explosive materials on the suspects' clothes that matched the type of explosive believed to have been used in the blast.
The three men had also been questioned over an explosion on October 5 on a rail line in Moscow's Biryulevo District, but were released due to lack of evidence.
Tuesday's blast damaged the rail line, leaving a left a two-meter hole in the track. The damage was repaired in around four hours.
