At least 60 people were injured in the incident, which prompted Russian prosecutors to launch a terrorist probe. Nineteen remain in hospital, one of them in a serious condition.
Russian Railways said repair work to the torn-up section of track, several hundred meters long, was completed early Wednesday morning, and that the restoration of power lines above the track was nearly complete.
The Nevsky Express, carrying 250 passengers, hurtled off the rails at 9:38 p.m. Moscow time (5:38 p.m. GMT) on Monday, near Veliky Novgorod, about 500 kilometers (300 miles) north of Moscow. Several carriages were overturned, and a 2-meter (6-foot) crater was left in the track.
The blast occurred just before a railway bridge over a road, but the train, traveling at around 190 kilometers per hour (118 mph), had sufficient momentum to make it over the bridge before running into the embankment, avoiding potentially massive fatalities.
As delays continued throughout Tuesday and Wednesday, passengers on the country's busiest rail route - popular with businessmen and tourists - had their work and holiday plans disrupted and missed flights.
Two passengers said they missed a non-refundable flight to Montenegro, and one family missed their plane to Egypt, forfeiting a $3,000 package holiday.
Under Russian Railway's rules, passengers are entitled to just 3% compensation of a ticket's value for each hour a train is delayed.
The president of the rail monopoly, Vladimir Yakunin, estimated the company's losses from the damage and delays at 250 million rubles ($10 million). Free food for passengers stranded in stations has so far cost the company 2.5 million rubles ($98,000), Yakunin told a news conference.
Russian Railways will have to spend around 150 million rubles (nearly $6 million) on repairing the 12 train cars damaged in the accident, and 100 million rubles ($3.9 million) on buying a new locomotive, he said.
Russian authorities have yet to reach any conclusions about the blast that derailed the train. Deputy General Prosecutor Alexander Bastrykin said Tuesday that investigators considered terrorism to be a likely cause, but said no conclusions had been reached.
Investigators said the bomb that derailed the train had a yield of three kilograms (about seven pounds) of TNT equivalent.
Lawmaker Nikolai Kovalyov, a former head of the Federal Security Service, said the incident could be connected to a military operation in Ingushetia, a volatile North Caucasus republic, where almost 2,500 Interior Ministry troops have been deployed to fight militants.
"This could have been an attempt to divert attention to another location - a method frequently used by terrorists," Kovalev told RIA Novosti. "Or else there could be quite a trivial explanation of boys playing war games."
Identikits were compiled Tuesday of two people seen near the tracks shortly before the explosion.