Wilbur Ross has a stake in Navigator Holdings, which transports oil and gas for Russian energy firm, Sibur.
The company makes millions every year and two major shareholders are under US sanctions.
Another shareholder is Kirill Shamalov, the son-in-law of the Russian President.
During his confirmation hearing in January, Ross testified he had cut all business ties that could present a conflict of interest.
Daniel Fried, an assistant secretary of state for European and Eurasian affairs under President George W. Bush, told the Guardian that Ross’ ties to Putin’s “cronies” could undermine US sanctions on Russia.
A spokesperson for Ross told the BBC’s Panorama: “Secretary Ross recuses himself from any matters focused on transoceanic shipping vessels.
They added the Secretary “works closely with Commerce Department ethics officials to ensure the highest ethical standards”.
Ross is a billionaire industrialist and has been a close friend of the President for a number of years and helped him avoid bankruptcy in the 90s.
The leaked documents are part of what has been dubbed the Paradise Papers, a massive trove of data from Appleby, a Bermuda-based legal services provider that helps establish offshore accounts and holdings.
It was obtained by the German newspaper Süddeutsche Zeitung, which called in the International Consortium of Investigative Journalists (ICIJ) to oversee the investigation working with The Guardian and the BBC’s Panorama amongst others.
There is no suggestion anything contained in the files is illegal but many of the revelations throw up huge potential conflicts of interest.
Ross’s offshore financial dealings will add further pressure on Trump as the Special Counsel investigation into links between his associates and Russia continues.
Also on Sunday it was reported the probe had enough evidence to charge the President’s former National Security Advisor, Michael Flynn and his son.
NBC News said Mueller’s team is looking at possible money laundering charges, lying to federal agents, and Flynn’s role in a possible plan to remove an opponent of the Turkish president from the United States in exchange for millions of dollars.
Mueller is increasing pressure on Flynn following his indictment of Trump campaign manager Paul Manafort, NBC News said.
Flynn served 24 days as Trump’s national security adviser but was fired after it was discovered he had misrepresented his contacts with a Russian diplomat to Vice President Michael Pence.
Barry Coburn, a lawyer for the younger Flynn, declined to comment. Robert Kelner, Flynn’s lawyer, did not immediately respond to a request for comment.
NBC said that Mueller’s office also declined comment.
It comes just days after former Trump campaign manager, Paul Manafort, was charged with, amongst other things, conspiracy against the US.