Commissioner Cressida Dick said they were looking into "potential breaches of Covid-19 regulations" in Downing Street and Whitehall since 2020.
Boris Johnson told the Commons he welcomed the investigation as it would "give the public the clarity it needs" over the allegations.
His spokesman also said the PM did not believe he had broken the law.
Dame Cressida said the investigation was launched after the Cabinet Office inquiry team, led by civil servant Sue Gray, passed information to the force.
It remains unclear whether the Met probe will delay the publication of Ms Gray's report, which had been expected this week.
Earlier, the prime minister's spokesman said parts of her inquiry would not be published until after the police investigation was completed.
But Downing Street later said talks about what is "suitable to publish" were still ongoing.
BBC political editor Laura Kuenssberg said the Met seem to have no objection to the full report being published, meaning it may be published sooner rather than later.
Dame Cressida would not say which parties were being investigated by the force, and while breaches of regulations can result in fixed penalty notices, the police inquiry did not mean they would be issued "in every instance and to every person involved".
Labour deputy leader Angela Rayner renewed calls for Johnson to resign in light of the inquiry, calling him a "national distraction".
Asking an urgent question in the Commons, she said "potential criminality has been found in Downing Street", and that the need for a police investigation into No 10 parties was "a truly damning reflection on our nation's very highest office".
But Paymaster General Michael Ellis called for MPs to "let the investigation run its course and not pre-empt its conclusions".
Johnson - who was in the Commons to deliver a statement on the situation in Ukraine - said: "I welcome the Met's decision to conduct its own investigation because I believe this will help to give the public the clarity it needs and help to draw a line under matters.
"But I want to reassure the House and the whole country that I and the government are focused 100 percent on dealing with the people's priorities, including the UK's leading role in protecting freedom around the world."
The news comes after fresh allegations of a birthday party being held for the prime minister in June 2020.
Downing Street has admitted that staff gathered inside No 10 to celebrate Johnson's birthday when the first Covid lockdown was still in place.
But ministers have disputed the number of people attending, and called for "patience" while Ms Gray's inquiry is carried out to establish the facts.
Dame Cressida said on Tuesday that she understood the "deep public concern" about the allegations of parties inside No 10, along with the "huge sacrifices" the public had made during the pandemic.
And she said it would "not normally be a proportionate use of time" for the force to investigate rule breaches as far back as two years, but police would look at allegations that "appeared to be the most serious and flagrant breach" of regulations.
She outlined the guidelines on when allegations of past breaches would be investigated, saying the factors the police considered were: Whether there was evidence that those involved "knew, or ought to have known that what they were doing was an offence", where not investigating "would significantly undermine the legitimacy of the law", and "where there was little ambiguity around the absence of any reasonable defence".
Dame Cressida said while the force would not give "a running commentary" on the case, they would provide updates at "significant points".
The Met later confirmed the probe would be led by its Special Enquiry Team, overseen by Deputy Assistant Commissioner Jane Connors, the force's lead officer for Covid.
Photo file Caption UK Prime Minister Boris Johnson