Senate investigation focuses on Harlan Crow's tax deductions for yacht used for Clarence Thomas's trips.

• The superyacht, Michaela Rose, of billionaire Harlan Crow is now the subject of fresh inquiries regarding the tax deductions he claimed for business purposes.
• Ginni Thomas and her husband Thomas have gone on multiple cruises, including voyages around Indonesia and New Zealand.
• Investigators from the Senate Finance Committee are examining Crow's financial and personal connections to Supreme Court Justice Clarence Thomas.

CNBC obtained documents showing that billionaire real estate executive Harlan Crow's super yacht was registered as a pleasure vessel with both U.S. and British maritime authorities, despite Crow reporting to the IRS that the mega yacht was a money-losing business venture during the same years.

The Senate Finance Committee is investigating Crow's financial and personal ties to Supreme Court Justice Clarence Thomas, as his use of a 160-foot yacht has attracted attention.

Ginni Thomas and her husband Thomas have gone on several cruises on the Michaela Rose, including trips to Indonesia and New Zealand. Thomas did not declare these expensive trips as gifts on his government disclosure forms, stating that they were personal trips with friends.

On Tuesday, Senator Ron Wyden (D-Ore.) wrote a 12-page letter to Crow's attorney, detailing new evidence that he claimed "raises serious concerns regarding the tax treatment of Mr. Crow's luxury assets, including tax deductions related to the personal recreational use of his superyacht for his benefit and that of his wealthy and powerful friends."

According to ProPublica, the Crow family claimed millions of dollars in business tax deductions for their yacht between 2003 and 2015, despite reporting it as an active yacht chartering business to the IRS.

For 10 out of the 13 years that ProPublic has records, Rochelle Charter, Inc., a company established by the Crow family to rent out a yacht, reported tax-deductible business losses.

To deduct business losses from federal income taxes, a company must have paying customers and be conducting an actual business.

In his letter to Crow, Wyden argued that it is not suitable for a taxpayer to claim to the Internal Revenue Service that a superyacht with registrations indicating it is not involved in trade can incur losses from supposed for-profit yacht charter services.

Harlan Crow's office spokesman responded to CNBC's request for comment on the deductions, stating whether there is any evidence that Michaela Rose has ever chartered or registered the yacht as a commercial vessel.

The spokesman stated that Mr. Crow employs professional accounting firms to prepare his tax returns and adheres to tax laws in good faith. Any accusation to the contrary is unfounded and damaging.

The spokesman stated that the politically motivated fishing expedition lacks a legitimate legislative basis and that Congressional Committees are not tax auditors or law enforcement officers. He added that targeting a private citizen for political purposes is highly inappropriate and unconstitutional, and sets a dangerous precedent.

Despite sailing under a British flag, the Michaela Rose is not registered as a commercial charter vessel in the U.K.

A spokesperson for the UK's Maritime and Coastguard Agency informed CNBC that the Michaela Rose is classified as a pleasure vessel under Part 1 of the UK Ship Register.

According to British merchant shipping regulations, pleasure vessels are used for leisure activities and do not generate income.

In the United States, the Michaela Rose is classified as a "pleasure boat" rather than a commercial vessel, according to government documents reviewed by CNBC.

The US Coast Guard official informed the Senate Finance Committee that Michaela Rose has not received a certificate of documentation to engage in coastal trade in the United States, including offering commercial charter boat trips.

It is unclear how the Michaela Rose carried out the commercial chartering business if it did not register as a commercial vessel or obtain certificates and waivers.

Wyden stated that any attempt to misrepresent a yacht used for pleasure as a business is a typical tax fraud.

Crow's lawyer did not respond to CNBC's request for evidence that Crow has ever rented out the yacht or registered it as a commercial vessel in any jurisdiction.

In 2014, after the death of his mother, Crow updated the interior of the yacht to a more contemporary style. According to ProPublica, Crow's tax information for that year revealed a $1.8 million loss from the company that operates the yacht, Rochelle Charter.