The $500 million Nord was heading for the South African port of Cape Town, Reuters reported.
The billionaire, who is close to Russian President Vladimir Putin, was among a number of Russians hit with sanctions by the US and EU after Russia's invasion of Ukraine.
His 141-metre vessel's prominent spot in the city's Victoria Harbour had sparked criticism from the US State Department in recent weeks.
Several Russian superyachts have been seized from ports around the world since the invasion began in February.
In August, the $75 million Axioma, allegedly owned by Dmitry Pumpyansky, was auctioned by Gibraltar.
In June, the $325 million Amadea, linked to oligarch Suleiman Kerimov, was seized by the US and arrived in San Diego Bay in California.
And in April, German authorities impounded Russian billionaire Alisher Usmanov’s superyacht Dilbar after determining it was legally owned by his sister, who is also subject to western sanctions.
The Nord arrived in Hong Kong on October 5 and has spent 15 days untouched in its port after a seven-day voyage from Vladivostok in the Russian Far East, through the Sea of Japan and the East China Sea.
The Hong Kong government did not immediately respond to questions on Thursday night.
The vessel was placed by MarineTraffic in waters south-east of Hong Kong early on Thursday evening. It appeared to be heading into the South China Sea.
A witness saw a fuel barge alongside the vessel inside the harbour at noon.
Hong Kong leader John Lee said on October 11 that the city's authorities would not act on unilateral sanctions imposed on Mr Mordashov by individual jurisdictions.
“We cannot do anything that has no legal basis,” said Mr Lee, who himself has been sanctioned by the US for his role in a crackdown on local freedoms.
Mr Lee, who is due to host an international investment summit in November with global business leaders, said the Chinese-ruled city would only abide by UN sanctions.
Reuters contributed to this report