Rev Andrew Foreshaw-Cain is calling the removal of the rainbow flag at St James Church in Kilburn a homophobic attack.
It is the third time one of the two LGBT flags has been taken down in two weeks.
Rev Andrew told Premier the flags are now being flown again.
He said: "The flags are up and they'll stay up and we won't be intimidated and nor will we allow our voice on this issue to be silenced.
"I think the fact that we will not allow ourselves to be intimidated or the flag to be taken down is a very positive thing."
The raising of the flags. pic.twitter.com/D8k6tFGndo
— Andrew Foreshew-Cain (@churchnw6) October 15, 2016
The openly gay vicar told Premier whoever removed it was violent: "The flags were cut down again, and the people who did this also ripped down some improved security we'd put on the church - they did it with quite a degree of violence."
He also said he had been receiving hate mail in the post over the last few weeks.
Flags back up. And we will not be intimidated. No surrender. pic.twitter.com/RLYujc63Ri
— Andrew Foreshew-Cain (@churchnw6) October 16, 2016
Fr Andrew told Premier everyone is welcome as his church.
He said: "We are an open an accepting congregation, that's one of the things that defines this particular community.
"Personally, I believe that is what the Gospel is telling us, and where the Holy Spirit is leading us."
