The Nobu chain, which has 21 restaurants on four continents and is the haunt of celebrities such as Madonna, Kate Winslet and Leonardo DiCaprio, was targeted by undercover investigators from the environmental group Greenpeace.
At three Nobu restaurants in London, investigators ordered tuna dishes described on the menu only by Japanese terms for the cut of the fish they were from.
The investigators asked that staff to identify the tuna species used, for Nobu does not specify on its menus which species of tuna it serves.
Samples were later tested to determine the type and it was found that dishes from all three were Atlantic bluefin.
The distinction is important because the Atlantic bluefin and the southern bluefin are listed as critically endangered by the International Union for the Conservation of Nature's Red List because of overfishing.
Although it is not illegal to serve Atlantic bluefin, also known as northern bluefin, many chefs, including Gordon Ramsay, have dropped it because of concern that fishing is at higher levels than stocks can withstand.
At Nobu Berkeley St, which has one Michelin star, investigators ordered for Atlantic bluefin (hon maguro in Japanese) but staff told them the restaurant did not stock it.
However, DNA tests have show that the fish they were given was indeed Atlantic bluefin.
At Ubon, Canary Wharf, also owned by Nobu, investigators asked for Atlantic bluefin and were served a dish that did not test conclusively either way.
However, a second dish they ordered, described only as "o-toro", the fattiest belly meat, was Atlantic bluefin.
At Nobu London, a waitress told the investigators that a dish on the menu was hon maguro. The fish that was served tested positive as Atlantic bluefin.
The lack of clear information about the species of tuna on sale at Nobu could land the restaurants in trouble.
A rep for Westminster city council said that falsely describing food was an offence.
"Nobu and Robert De Niro are clearly making a great deal of money serving up endangered fish," the Telegraph quoted Willie Mackenzie of Greenpeace, as saying.
The restaurant refused to comment on the matter.