TOKYO—Five workers at a Japanese nuclear facility that handles plutonium have been exposed to high levels of radiation, after a bag containing highly radioactive material apparently broke during an equipment inspection, the Japan Atomic Energy Agency (JAEA) said on Wednesday.

The incident occurred on Tuesday at its Oarai Research and Development Center, a facility for nuclear fuel study that uses highly toxic plutonium. The cause of the accident is under investigation, the state-run agency said. It raised nuclear security concerns, as well as questions about whether the workers were adequately protected.

The agency said its initial survey found contamination inside the nostrils of three of the five men, a sign they had inhaled radioactive dust. All five were also found to be contaminated on their limbs after removing protective gear and taking a shower, which would have washed off most contamination.

Agency Spokesman Masataka Tanimoto said one of the men had high levels of plutonium exposure in his lungs. The worker, in his 50s, had opened the lid of the container when some of the 300 grams of plutonium and uranium in the broken bag flew out.

Internal exposure poses a bigger concern because of potential cancer-causing risks. The man’s exposure, 22,000 Becquerels, could mean the effect on his lungs may not be immediately life-threatening but would add up over time, and he will need to be regularly monitored, said Makoto Akashi, a doctor at the National Institute of Radiological Sciences, where the workers are being treated. Nuclear Regulation Authority Chairman Shunichi Tanaka blamed work routine complacency as a possible cause. Regulators have started investigating possible violations of safety standards at the facility.

JAEA has a poor safety record at Monju, a plutonium-burning fast breeder reactor that it oversees. The government recently decided to scrap Monju, which suffered a major accident in 1995 and has since hardly operated.

Japan’s possession of large plutonium stockpiles, from the country’s struggling nuclear spent-fuel recycling program, has faced international criticism. Critics say Japan should stop extracting plutonium, which could be used to develop nuclear weapons.

To reduce the stockpile, Japan plans to burn plutonium in the form of mixed oxide fuel, fuel—a mixture of plutonium and uranium—in conventional reactors. But the restarting of halted nuclear plants has proceeded slowly amid persistent anti-nuclear sentiment since the 2011 Fukushima nuclear-reactor meltdown caused by a massive earthquake and tsunami.