Rescuers, meanwhile, continued to sift through the wreckage of the four carriages because not all passengers had been accounted for.
At least 250 passengers, many of them schoolchildren returning from a ski trip, were believed to be on the train when it crashed, in what was among the deadliest European train accidents in 25 years.
The train derailed Monday afternoon near Bioce, a village about nine miles northeast of Podgorica, as it emerged from a tunnel above the Moraca River, police said. The train plummeted into a 330-foot deep ravine in the river canyon.
Initial reports indicated the train's brakes may have failed, Interior Minister Jusuf Kalamperovic said. The injured train driver was under police custody in hospital, suspected of negligence, but no other details were immediately available.
There were 90 children among the injured, said Miodrag Djurovic, the head of the main Podgorica hospital. Earlier, the death toll was reported at 44 because another hospital patient who died was mistakenly counted among the passengers, Djurovic said.
Meanwhile, a 17-year-old passenger gave birth to a boy Tuesday at the hospital after her injuries induced premature labor.
Overnight, darkness in the densely forested area hampered rescue efforts. Victims had cried for help from the ravine.
"The train simply went wild, out of control," a man said as blood poured down his forehead. "I was fine because I was in a back compartment, those in the front got the worst of it."
Grieving relatives lined up outside an improvised tent at the Podgorica hospital morgue Tuesday morning to identify the dead and take their bodies home.
"I lost my whole life in this tragedy," sobbed Radomir Cobarkapa, 50, from the village of Tomasevo. His wife and son were killed and two of his other children were injured in the crash.
Tarzan Milosevic, the mayor of Bijelo Polje, came to claim the bodies of 24 people from the northeastern town killed in the accident. The bodies would be taken to a community hall in Bijelo Polje later Tuesday.
"There are no words to describe this," he said through tears.
Deputy Prime Minister Miroslav Ivanisevic described the crash "as the worst rail accident in the history of Montenegro."
Montenegro's transport minister, Andrija Lompar, resigned because of the accident, Ivanisevic said. Head of Montenegro railways, Ranko Medenica, also resigned.
A three-day mourning period was announced for the victims.
The train was en route from Bijelo Polje to the Montenegrin coastal city of Bar when it derailed near Podgorica.
"I had fallen asleep when a loud noise woke me," said Stanislava Bukovic, 60, one of the injured passengers, as she was carried away on a stretcher. "Then I felt something hit my head and lost consciousness. The next thing I knew I was on this stretcher."
Serbia-Montenegro President Svetozar Marovic said the accident was a "great tragedy" for Montenegro.
Emergency crews had "reacted as well as could be expected in such a harsh and inaccessible terrain," Montenegrin Prime Minister Milo Djukanovic said while visiting Podgorica hospital.
EU envoy and Slovak diplomat Miroslav Lajcak, sent by Brussels to mediate in the internal Montenegrin dispute over independence, visited the injured and offered to give blood.
Other deadly train accidents in Europe in recent decades included the June 1998 derailment of a high-speed train traveling from Munich to Hamburg, which killed 96 people. A crash in a dead-end tunnel at Moorgate Underground station in central London killed 43 in February 1975.