The images, taken Saturday, show the Rye Song Gang 1 appearing in the dark of night beside a Dominican-flagged ship, the Yuk Tung. The two ships then are seen sailing away from each other after the sun rises on Saturday morning.
"The (Japanese) government strongly suspect the two engaged offshore delivery which was banned by UN Security Council resolutions," the ministry said in a statement.
It's not the first time that the the Rye Song Gang 1 has been accused of engaging in illicit ship-to-ship transfers. The US Treasury Department released images of the ship
allegedly conducting a transfer on October 19. It did not name the other ship involved, but the South Korean Foreign Ministry said it seized a Hong Kong-registered vessel, the Lighthouse Winmore, for transferring refined oil to a North Korean ship that same day.
The Rye Song Gang was among eight ships banned from entering ports from across the globe in late December
for violating UN sanctions on North Korea.
"To have these large vessels engaged in this type of activity, that's troubling," said John Park, the director of the Korea Working Group at Harvard University's Kennedy School of Government.
"The scale of it is much larger than previously thought ... when it comes down to it actually clamping down on this type of activity in a swift manner, you're going to have to manage expectations," he said.
, after Pyongyang conducted a sixth nuclear test, UN member states have been banned facilitating or engaging in ship-to-ship transfers with North Korean-flagged vessels.
When asked for comment about the latest allegation, Hugh Griffiths, the coordinator of the UN Panel of Experts on North Korea -- the body charged with monitoring sanctions enforcement and efficacy -- told CNN "this matter is already in under investigation, but it will be featuring in an upcoming report to the Security Council at the end of this month."
These ship-to-ship transfers appear to be a way to get around the port ban, according to Anthony Ruggiero, an expert in the use of targeted financial measures at the Foundation for the Defense of Democracies.
"All of this suggests that the US is going to have to go to the next level, which is declaring all North Korean vessels as suspect and reasonable grounds for inspection," Ruggiero, who previously worked at both the US State and Treasury departments, told CNN.
A series of increasingly strict resolutions were passed at the UN Security Council against Pyongyang in 2017, in response to the rogue regime's repeated weapons tests.
The measures, passed after intense lobbying by Washington, targeted energy, money transfers and shipping.
The Trump administration is waging what it calls a campaign of "peaceful pressure" on the regime of North Korean leader Kim Jong Un. It hopes that, as the international community ramps up sanctions and the diplomatic isolation on North Korea, Pyongyang will be squeezed hard enough that it will eventually put its nuclear weapons on the negotiating table in exchange for relief from sanctions.
North Korea has for years used deceptive shipping practices to bring in money and goods for the regime. But its fleet has come under increased scrutiny as the United States has looked for new ways to punish the Kim regime.
The issue of ship-to-ship transfers was brought up several times at a summit on North Korea in Vancouver earlier this month. US Secretary of State Rex Tillerson said that more was needed to be done on the issue of maritime interdiction operations when it comes to stopping sanctions violations.
"We must put an end to illicit ship-to-ship transfers that undermine UN sanctions," he said.
After the first set of pictures surfaced in South Korea media, US President Donald Trump said Beijing had been "caught red-handed" for violating UN measures on North Korea.
China has consistently denied breaching sanctions.