President Vladimir Putin blamed Chechen rebels for an explosion that tore through a Moscow subway car, killing at least 39 people and injuring more than 100 during rush hour Friday morning.

"We do not need any indirect confirmation. We know for certain that [Chechen leader Aslan] Maskhadov and his bandits are linked to this terrorism," Putin was quoted as saying in the Russian Interfax news agency.

A spokesperson for Maskhadov denied he was involved in the deadly blast.

Rescuers at the Paveletskaya metro station, Moscow (AP photo)

The Russian capital has been on alert for terrorist attacks following a series of suicide bombings that officials have blamed on Chechen rebels.

The Interfax news agency quoted police sources saying the attack was carried out by a female suicide bomber.

The news agency reported that police had a videotape of the suspected attacker and her accomplice standing on the platform before boarding the train.

Wreckage of the subway car.

But Moscow's Deputy Mayor Valery Shantsev said the bomb may have been planted in a suitcase or backpack on the floor of the subway car.

A severe fire broke out in the train as passengers were being cleared from Avtozavodskaya station, a little more than 250 metres from the site of the explosion.

The train was travelling northwest on one of Moscow's deepest metro lines to the Paveletskaya station. The blast occurred around 8:40 a.m. on the second car of the train.

Moscow police spokesperson Kirill Mazurin said that after the explosion, the train travelled for about another 500 metres before coming to a stop.

In December, a female suicide bomber blew herself up outside the National Hotel across from Moscow's Red Square, killing at least five others. Two suicide bombers blew themselves up at a Moscow rock concert in July, killing themselves and 14 other people.