Police officers visited Christ the King Polish Church in Balham, London, on Sunday to apologise for halting a Good Friday service.
The Easter service was broken up midway through by officers because they said worshippers "were clearly not socially distanced".
Worshippers were ordered to leave the building and threatened with £200 fines or even arrest if they failed to provide their details.
At the time, the church said the service had been held in keeping with government Covid-19 guidelines, and that "the police brutally exceeded their powers by issuing their warrant for no good reason, as all government requirements were met".
On Sunday, Detective Superintendent Andy Wadey and Superintendent Roger Arditti addressed worshippers and admitted officers were in the wrong.
He said: "The intention of the Met is to protect and support communities in staying safe during the pandemic.
"We know, however, that many people were very upset by what happened on Good Friday and we deeply regret that.
"Since then, there has been significant reflection and learning by me, Roger, our colleagues who work with us locally and also, senior leaders at New Scotland Yard.
"The Metropolitan Police truly wishes to serve and protect you in the very best possible way.
"I truly hope that today marks the start of a renewed, deep and lasting relationship with the parish of Christ the King Balham and also the wider Polish communities."
Churches were allowed to gather for worship during the lockdown, with numbers limited to how many could safely fit in the building following social distancing guidelines.
Responding to the apology, the Catholic Archbishop of Southwark, said there had been "very fruitful" conversations with the police since the incident and that the church remained committed to "healing" and "collaboration".
"We all share the same desire to move forward in friendship, working together for the common good. We are committed to enabling freedom of worship for everyone, in safe and secure environments," he said.
Mgr Władysław Wyszowadzki, priest of Christ the King, added, "The interruption of the Good Friday liturgy was very painful for our parish community, but in the spirit of the Gospel, we willingly extend our hand to the representatives of the police authorities in order to further build a deep and lasting relationship between us, based on mutual respect and regard for the rights of worshippers to freely practice their faith."