The accountancy firm said the note “was not a Deloitte point of view”, while acknowledging the “disruption” it had caused Downing Street.
Read more: Big Four audit giant dragged into Brexit row
The memo was critical of the Prime Minister's style of leadership, and said businesses would be able to “point a gun at the government’s head”.
It also claimed the government and civil service were completely unprepared to cope with the scale of Brexit, saying an additional 30,000 staff members were needed.
The Prime Minister’s office had sought to distance themselves from the memo, saying it was an “unsolicited document”.
Deloitte’s apology says the note, written by one of its consultants, was for “internal audiences” only.
The statement from Deloitte said: “Deloitte regrets the publication of the two-page note, and has apologised for the unintended disruption it caused Government.
“The note was for internal audiences and was not a Deloitte point of view. We have put forward a plan for working with Central Government to put this matter behind us.”