A spokesperson said that the situation was ongoing at 1pm, as the first parts of the UK were hit by a fresh storm expected to sweep across the country this weekend.
“HM Coastguard is coordinating a search and rescue mission after reports of a man overboard from a vessel off Margate Harbour,” a spokesperson said.
Lifeboats, a helicopter and a police boat have also been dispatched, they said.
The distress call – received around 5.40am - is believed to have come from B Gas Margrethe, a Maltese tanker that had been anchored off the coast of Margate.
The urgent search operation comes as the UK prepares for its second blustery weekend in a row with Storm Dennis.
The Met Office has issued severe weather warnings over heavy rain and strong winds, with large parts of the country threatened with flooding.
Hundreds of UK flights have been cancelled over the bad weather, which is forecast to move through the country over the weekend.
Forecasters were expecting winds to reach 70mph along coastlines.
However, a Met Office spokesperson has warned that rainfall could cause the most problems this weekend, with northwest England seeing some of the heaviest showers.
Members of the British Army have been sent to help locals deal with the fresh storm in West Yorkshire, which was one of the areas badly hit by flooding during last week's Storm Ciara.
Thousands of homes were left without power and 90mph winds were recorded around the UK during the previous bout of bad weather.
Additional reporting by Press Association