Allegra Stratton said Mr Johnson’s attendance was “incredibly important” despite Sir Keir issuing apology over his own visit a month later.
The Labour Campaign for LGBT+ Rights said Sir Keir’s visit was “unacceptable” and he has since said it was a “mistake” to visit the church.
The church recently opened up part of its premises as a vaccination centre and visitors in recent weeks have included the Prince of Wales. However, the church’s senior pastor, Agu Irukwu, has previously been criticised after speaking out against same-sex marriage and equality laws.
Asked if the PM regretted his decision to visit Jesus House, Ms Stratton said: “We remember the visit to Jesus House well because that day it was the site of a pop-up centre for vaccines.
“One of the main jobs inside Government over the last few weeks and months has been driving up vaccine take-up in communities that are hesitant about taking it – most noticeably the black community. That was the purpose of his visit that day.
“It was a profitable visit where he was able to meet black community leaders and work to increase vaccine take-up and deal with vaccine hesitancy.
“So it was an incredibly important visit, making sure every aspect of the population feels confident in and takes the vaccine is a top priority for this government.”
She said the Government was “fully committed” to advancing LGBT rights and championing equality.
Sir Keir said: “I completely disagree with Jesus House’s beliefs on LGBT+ rights, which I was not aware of before my visit. I apologise for the hurt my visit caused and have taken down the video. It was a mistake and I accept that.”
The LGBT+ Labour group later said it believed the explanation was a “genuine mistake” where “research had mistakenly not been carried out in advance of the visit”.