A massive security operation involving up to 13,000 police paid off as the low-loaders carrying the 12 containers of waste rumbled without incident into the facility at Gorleben, northern Germany, before dawn.
Overnight, police had dispersed around 500 anti-nuclear campaigners who had gathered at a nearby village in a last-ditch effort to block roads being used by the transport.
Several water cannon and a heavy police presence were on standby and while scores of people were briefly detained, ostensibly to let the convoy pass, no major incidents were reported.
Afterward, regional interior minister Uwe Schuenemann said police had taken a total of 256 people into temporary custody over the past few days.
He said the protests had generally passed off peacefully, and estimated the cost to Lower Saxony state at about 25 million euros (29 million euros), five million less than last year.
Since Germany decided to phase out atomic energy, the protests have been a far cry from the chaotic heyday of the 1990s when there were frequent clashes with police and convoys were significantly delayed.
The number of protestors has steadily decreased since the tens of thousands of a few years ago and certainly do not match the police presence.
Nor are clashes as violent as in the past, with only a few scuffles Monday and Tuesday as police removed protestors sitting down on the tracks.
Nevertheless, the environmental group Greenpeace said the need for support was as strong, if not stronger, than ever.
"Radioactive waste can contaminate the ground water here in the long-term," said Mathias Edler, a nuclear expert for the group.
A campaigner with X-tausendmal, a German environmental group, said some of the fall in numbers was because members of the Greens were less active now the party is part of the ruling coalition.
She also said that since the September 11, 2001 attacks against the United States, "people have been protesting against the (Iraq) war and nuclear arms, and therefore less on nuclear waste transport."
Like other activists, the woman, who did not want to be named, claimed she could detect growing interest in the issue once again.
Greenpeace's Edler said he was notably struck by the number of young people taking part in the protests.
Despite the low turnout, local activist Dieter Metk was satisfied.
"The 12 Castor containers were still delayed by around six hours," he said. "This can be deemed a success."
The consignment, which had Sunday left a reprocessing plant at La Hague in northwest France, was dogged by protests along the route. The spent fuel rods had been sent there because Germany has no treatment facilities of its own.
Among those arrested were two people who chained themselves to the tracks, while according to medical officials, a total of 70 people were injured during the various protests.
Greenpeace accused the police of using excessive force. They in turn blamed activists for throwing bottles and hitting officers with planks.
The operating company at Gorleben said that the containers would be placed in temporary storage before being moved to their permanent positions over the next several weeks until mid-January.