In her inquiry into lockdown-breaking gatherings at Downing Street under Johnson, senior civil servant Sue Gray condemned some of the behaviour in government as being "difficult to justify".
But she also said she could not offer a "meaningful report" - an apparent acknowledgement of a police investigation into other gatherings which led to only an abridged version of the report being released.
These include one in the prime minister's flat above his Number 10 office.
Johnson, who is facing the gravest threat to his premiership, appeared in parliament following the report's publication.
"I want to say sorry," Johnson said parliament.
"I get it and I will fix it."
Gray's report looked into what has become weeks of a steady drip of stories about events in Downing Street during the COVID-19 lockdown, with reports of aides stuffing a suitcase full of supermarket alcohol and dancing until the early hours.
However, parts of the report were not published due to the ongoing police investigation, which could take months.
He has so far weathered calls from opponents and some in his own party to resign by saying people needed to wait for the report.
"At least some of the gatherings in question represent a serious failure to observe not just the high standards expected of those working at the heart of government but also of the standards expected of the entire British population at the time," Gray wrote.
She also said the "excessive consumption of alcohol" at Downing Street was not appropriate.
"Against the backdrop of the pandemic, when the government was asking citizens to accept far-reaching restrictions on their lives, some of the behaviour surrounding these gatherings is difficult to justify," it said.
Gray was asked to investigate more than a dozen gatherings - including a "bring your own booze" party in the Downing Street garden - at a time when millions were kept apart from friends and relatives for months because of the restrictions.
Since the police investigation was opened last week, Gray said in her so-called update that she could only now refer to four events, rather than the 16 she initially considered to make sure she did not prejudice the probe.
"Unfortunately, this necessarily means that I am extremely limited in what I can say about those events and it is not possible at present to provide a meaningful report setting out and analysing the extensive factual information I have been able to gather," she wrote.
One of the events which she was forced to leave out was a gathering on November 13 in Johnson's Downing Street apartment above government offices, and one of the most damaging allegations of the "bring your own booze" party on May 20, 2020.
"As I have noted, a number of these gatherings should not have been allowed to take place or to develop in the way that they did," she said in the report.
Opponents were critical of the limited nature of the report and renewed their calls for Johnson to quit.
"Everyone knows Boris Johnson broke the rules and lied to the country," Ed Davey, leader of the opposition Liberal Democrat party, said.
Angela Rayner, deputy leader of the main opposition Labour Party, said she found the report "sickening".
"It is the most fundamental failure of any prime minister and I'm absolutely shocked that Boris Johnson can even show his face in parliament today," she told Sky News.
"He should be resigning because he has lost the confidence of the British people."
The prime minister's spokesman has said that Johnson does not believe he has broken the law.
Johnson has apologised for errors that were made and said he attended one garden party thinking it was a work event, but has rejected calls to quit.