As the Rossita pulled away from the pier at Andreyeva Bay, sounding a long boom of its horn, a military band struck up a jaunty march. On board the ship were nine sealed metal casks, each four metres high and weighing 45 tonnes, containing canisters of spent nuclear fuel. Dozens of Russian and foreign nuclear specialists looked on applauding, as the chilly rain of a northern summer fell on the bay deep inside the Russian Arctic.

The ceremony, held on Tuesday afternoon, marks the culmination of a long international project to begin removing nuclear fuel from the site, formerly a top-secret Soviet installation. Nuclear specialists say Andreyeva Bay contains the largest reserves of spent nuclear fuel in the world, in fragile conditions that have disturbed the international community for years.

During the Cold War period, nuclear submarines were refuelled at sea, and the spent nuclear fuel was then shipped to Andreyeva Bay, where it was placed in a special storage facility to cool off before being transported to a reprocessing plant at Mayak, in the Urals. But in the early 1980s, leaks sprung up in the storage system, causing high levels of radioactive contamination.

When the Soviet Union collapsed, transfers of the spent fuel ceased, and about 22,000 spent nuclear fuel caskets were left at Andreyeva Bay in leaky dry storage units, creating the potential for an environmental catastrophe.

“I’ve been all over the world to pretty much every country that uses nuclear power and I’ve never seen anything so awful before,” said Alexander Nikitin, a former naval officer and environmentalist who has been monitoring the site for years.

“With nuclear material, everything should be done very carefully, and here they just took the material and threw it into an even more dangerous situation.”

In the decade after the Soviet collapse, the main concern was that poorly maintained facilities could lead to an onsite disaster. Nearly 250 nuclear submarines were decommissioned in the aftermath of the Soviet collapse, and facilities such as Andreyeva Bay were left in a perilous state.

“There wouldn’t have been a big explosion, but it could still have been something serious,” said Nikitin. “With nuclear fuel, once processes start, you have no way of knowing how they will develop.”

Over the next decade, security fears also increased. “Before 9/11, nobody would really think anyone would be crazy enough to try to handle spent nuclear fuel, but with the new type of terrorist threat we face, this became a bigger worry,” said Balthasar Lindauer of the European Bank for Reconstruction and Development (EBRD), which has managed the donor funds from western countries to help with the clean-up.

The facility at Andreyeva Bay was one of many top-secret installations in the Soviet Arctic. A two-hour drive from the regional centre of Murmansk along a road cut out of mossy rocks, still dusted with snow in late June, the entire area around Andreyeva Bay is closed to all foreigners and even Russians who are not registered there. A heavily armed military checkpoint on the outskirts of town keeps out all those who do not have security clearance . This is partly because Russia has a working nuclear submarine base on the other side of the bay at Zaozyorsk.

It might seem odd that, as Russia ploughs more money into its current military budget, western nations who see Moscow as a military threat are helping to fund the clean-up of the mess the Soviet military left behind. 13 countries have provided €165m in funding since 2003 for nuclear decommissioning in Russia’s north-west. There have also been a number of bilateral projects, with Britain, Norway and other countries funding a long project to help clean up Andreyeva Bay.

The Norwegian foreign minister, who was present at Tuesday’s ceremony, said the funding for the project was committed nearly two decades ago, when Russia was in no economic state to deal with the problems alone. He also pointed out that the Andreyeva Bay facility is only about 40 miles from the Norwegian border, making the decommissioning issue one in which Norway has long taken a strong interest.

“Nuclear challenges recognise no borders, and it is in our common interest to deal with nuclear waste now rather leaving the problems to future generations,” said the Norwegian foreign minister, Børge Brende.

A suite of new buildings has been constructed around the area where the spent nuclear fuel caskets are kept, replacing the decaying structures that stood there previously. Work to load canisters into the giant protective casks can now be done using specially commissioned machinery.

The Rossita, a ship constructed for the task, will take the huge fuel casks to Murmansk, where they will be put on fortified trains which will proceed under armed guard on the long journey from the Arctic to the Mayak reprocessing site. At the Mayak facility, the spent fuel will be recycled and the Russians say they will turn it into fuel to be used in civilian nuclear reactors.

Specialists at the plant estimate it could take 10 years to remove all the fuel. About half of the caskets have some kind of surface damage to their containers and will be dealt with after the non-problematic batches have been removed.

“This is the end of a long process, but also the beginning of another long stage in the clean-up,” said Marina Kovtun, the governor of Murmansk region. “Despite international tensions, work went on every day. Everyone who was working on this project understood that they were doing this for all of humanity and for protecting our environment.”

Indeed, in the current climate of hostility between Russia and the west, it was an unusual tale of bonhomie and cooperation, as the ceremony included the flags of 10 western nations as well as the Russian tricolour.

“The Barents Sea is maybe the cleanest sea in the world, and if something had happened here, it would have affected the whole Arctic,” said Brende. “This process is not completely without risk, but compared to doing nothing, the risks are now much lower.”