Simon Case only became aware of the plans in late February, after a news story was published appeared about the Prime Minister’s difficulty funding the renovation, the Times reported.
Mr Case, who was appointed cabinet secretary last September, is now playing a leading role in handling the fallout over the refurbishment.
Mr Johnson’s former chief adviser Dominic Cummings last month said he had told the PM that his plans “almost certainly broke the rules” on the disclosure of donations.
The Electoral Commission has launched an investigation
A spokesman for the Cabinet Office confirmed that the civil servant was not told about the plan until newspapers uncovered it.
“The cabinet secretary only became aware of the trust in late February,” the spokesman told the Times.
The spokesman said, however, that other civil servants had been aware of the trust, saying: “Cabinet Office officials have been engaged and informed throughout and official advice has been followed.”
Case is now conducting a review into the arrangements. It will feed into another review by Lord Geidt, the independent adviser on ministers’ interests.