Ross has also been a long-standing donor to the Conservative Party, pledging 250,000 pounds in the last election campaign.
"Mr Ross facilitated accommodation for Mr Johnson on Mustique valued at £15,000".
In the register, Johnson wrote that he had accepted "accommodation for a private holiday for my partner and me, value £15,000", as a benefit in kind.
"What is being said in the letter has been covered off by additional statements made by David Ross' spokesman", the source told the PA news agency.More news: LeBron, Giannis choose teams for NBA All-Star Game
The register also shows earnings Mr Johnson received past year before becoming PM, including more than £327,000 for seven speaking engagements, one of which was a three-hour speech where he was paid £122,899.74.
Mr Johnson declared the trip on the Register of Interests, in which Members of Parliament must state any benefits received.
But last night Mr Ross insisted that he was not the owner of the villa and had not paid for Mr Johnson's stay.
Lord Peter Ricketts, who was the UK's National Security Adviser between 2010 and 2012, said the prime minister should have realised that "the world doesn't stop over Christmas and New Year", and said Johnson was "caught short" by the diplomatic crisis.
'This was a benefit in kind from David Ross, a friend and former colleague.
Labour asked the Parliamentary Commissioner for Standards to investigate who was behind the donation.More news: Lionel Richie tells 'American Idol' contestant: 'I don't like you'
If all transparency requirements have been followed, what is the source of the discrepancy and confusion between the account provided by Mr Ross and the Prime Minister's insistence that the rules have been followed?
The holiday lasted from December 26 to January 5, according to the entry, and Ross was named as the financial provider.
Johnson, who wanted to minimise any disruption from the cabinet reshuffle, quickly appointed Javid's deputy Rishi Sunak, an ultra-loyal supporter of the prime minister who has often been put in front of the cameras to sell government policy.
He added: "transparency is crucial to ensuring that the public have confidence that elected Members of this House have not been unduly influence by any donations or gifts that they may receive".
Mr Johnson faced criticism over his holiday for not returning sooner, after the USA killing of Iranian general Qasem Soleimani raised tensions in the Middle East.
Shadow foreign secretary Emily Thornberry accused Mr Johnson of "sunning himself" while leaving cabinet secretary Mark Sedwill to chair three emergency Cobra meetings amid growing tensions following the killing.More news: USA expects that OPEC will continue to cut oil production in 2020