The Russian president, Dmitry Medvedev, has ordered an investigation after a nuclear submarine caught fire during repairs in the Arctic, injuring at least nine people.

The blaze, believed to have been started by a welding lamp igniting rubbish and wooden scaffolding next to the craft, raged for nine hours at a shipyard in the Murmansk region. Up to 30 crew members remained inside the submarine, although it was unclear if they were trapped.

Russian officials were quick to announce there had been no radiation leak from the nuclear sub, named Yekaterinburg, after the flames were extinguished. Conflicting reports said between nine and sixteen people were treated for smoke inhalation. Bellona, a respected Norwegian NGO which monitors Russia's nuclear fleet, said the number of casualties may have been higher.

Friday's fire was the second blow for Russia's military this week after it emerged a blogger had published photographs of a night visit to a secret rocket engine factory near Moscow. It is also the latest in a string of accidents to befall Russia's fleet of nuclear submarines in recent years, the most notorious being the explosion that sent the Kursk to the bottom of the Barents Sea in 2000, killing all 118 crew on board. A K-159 submarine sank in the same waters three years later with the loss of nine men, and 20 people died after the leak of a fire suppressant gas on a K-152 Nerpa off Russia's Pacific coast in 2008.

The K-84 Yekaterinburg, launched in 1984, is normally equipped with up to 16 missiles and 12 torpedoes. It was reportedly unarmed and in dry dock when the fire started Friday afternoon and spread to the rubber shell around the craft. About 400 emergency workers struggled to contain the blaze using helicopters and tug boats, partially submerging the vessel in order to put it out.

The 18,200-tonne, 167-metre Yekaterinburg was reportedly used twice this year to successfully test-fire the Sineva ballistic missile, also known by its Nato designation Skiff.

Igor Konashenkov, a defence ministry spokesman, said the Yekaterinburg's reactor was out of operation at the time of the accident, which happened at the Roslyakovo dock, one of the main port's for Russia's northern fleet, situated about 900 miles north of Moscow close to the city of Murmansk. "There is no danger of a radioactive leak," he said.

Prosecutors have launched a criminal investigation into the accident. Medvedev ordered deputy prime ministers Dmitry Rogozin and Igor Sechin to examine the causes of the fire and ensure the craft is restored.

The fire will embarrass Medvedev, who this year approved £400bn of arms spending to 2020.

The desolate region around Murmansk contains the biggest concentration of old nuclear reactors in the world and, since the cold war ended, has become the world's atomic dustbin. Murmansk is home to the old Soviet Union's northern fleet of nuclear submarines, many of Russia's atom-powered icebreakers and several 40-year-old civil reactors.

Alexander Ruzankin, head of economic development for the Murmansk region, says it has around 200 working nuclear reactors and 20,000 separate stores of waste, ranging from containers full of radioactive water to decrepit buildings full of fuel rods.

Nearly 20% of the world's reactors and nuclear fuel is concentrated in the region. A few obsolete nuclear submarines are decommissioned each year with the help of US and Norwegian aid, but the nuclear legacy is growing as Germany and former Soviet states send their radioactive research reactors and nuclear waste there for decommissioning and eventual shipment to the Urals.

Many of the stores are in a dangerous condition and are leaking water and radioactive substances into the soil and water.