More than 300 people had crammed into the makeshift venue and police were forced to deploy a helicopter and dogs in order to disperse the partygoers.
The following month, 70 people were given FPNs for attending two house parties held in the same street in upmarket Mayfair in central London.
But it is thought no other venue in the country has seen as many fines issued as Downing Street.
Confirming the latest update, which was delayed until after the May local elections were out of the way, a Scotland Yard spokesman said: "As of Thursday, May 12, Operation Hillman, the investigation into breaches of Covid-19 regulations in Whitehall and Downing Street, has made more than 100 referrals for fixed penalty notices (FPNs) to the ACRO Criminal Records Office.
"These referrals have continued to be made throughout the period since our last update on Tuesday, April 12, and the investigation remains live."
The Metropolitan Police refused to confirm which events the latest fines covered, but it is understood a large number were handed out to attendees of a Christmas cheese and wine party held in Downing Street.
Number 10 staff had drinks and even held a Secret Santa at the event on December 18, 2020.
Johnson was not present at the gathering, but when a video emerged showing officials joking about it, Allegra Stratton, his former press secretary was forced to resign.
It is also thought fines have now been issued to some of those who attended the infamous garden party held at Number 10 in May 2020.
An email sent by Martin Reynolds, the Prime Minister's Principal Private Secretary, told people to "bring your own booze" at a time when all social gatherings were banned.
The email read: "Hi all. After what has been an incredibly busy period it would be nice to make the most of the lovely weather and have some socially distanced drinks in the No 10 garden this evening. Please join us from 6pm and bring your own booze!"
Mr and Mrs Johnson did attend the garden party briefly, but neither have received a fine in connection with the event.
Last month it was confirmed that the couple had both been handed a £50 fixed penalty notice for attending a party to celebrate the Prime Minister's 56th birthday on 19 June 2020.
Rishi Sunak, who was among those at the gathering, also received an FPN, which he accepted and paid.
Scotland Yard investigating 12 events
Scotland Yard detectives are investigating 12 events that took place in Downing Street and Whitehall on eight separate dates between May 2020 and April 2021.
Fines have so far been issued to attendees of a raucous karaoke party in June 2020, which included Helen Macnamara, who was Whitehall's head of ethics at the time.
A leaving party for Kate Josephs, the government official who was in charge of writing the Covid laws, is also one of the events for which fines have been handed out.
Simon Case, the Cabinet Secretary, has not received a fine, despite reportedly being in attendance at some of the events being investigated by Scotland Yard.
The Prime Minister's official spokesman said: "With regards to the Cabinet Secretary and the Prime Minister, I don't have any update ... the position (is) we will update you if that were to change."
He added: "You'll know that the Prime Minister has on a number of occasions apologised and made clear that there were things we simply did not get right, and that he is sorry for how this matter has been handled.
"Obviously that remains the case. And like I say, he will have more to say at the conclusion ... and when the Sue Gray report is published."
Asked about the latest fines as he arrived for a cabinet meeting in Stoke-on-Trent on Thursday, Johnson said he was "sure we'll have plenty to say about that when the thing's finished".
