The proposed new law would allow undercover agents, from the security forces or police, to commit certain crimes undercover without facing prosecution. It responds to concerns a blanket ban on agents breaking the law could leave them vulnerable to detection from the groups they are infiltrating.
Sir Keir instructed his MPs to abstain on the motion which was voted through on Monday night.
However, 18 Labour MPs defied this order and voted against the bill.
These included former leader Jeremy Corbyn alongside John McDonnell and Diane Abbott, who were appointed as his Shadow Chancellor and Shadow Home Secretary respectively.
In response to Sir Keir’s decision angry left-wing activists, many self-identifying as Labour members, got ‘#ResignStarmer’ trending on Twitter.
One activist from Cornwall, with nearly 24,000 followers, tweeted: “No more excuses.
“No more government support. No more quisling abstentions. I’ve no patience left.
“We need an opposition leader & it’s clear as day Starmer will never fit that bill. He has to go.”
Another activist added: “I say #ResignStarmer.
Ahead of the security bill vote Sir Keir defended abstaining and said Labour would attempt to alter the legislation at the committee stage.
Denying he’s losing control of his party Sir Keir said: “No, there are obviously strong views on this particular bill.
“It is important that the powers that are exercised are there in a statute. It’s the right thing.
“Obviously we want to see the bill strengthened and we will be focusing on that.
“But we do need that bill to put those powers on a statutory footing.”
According to BBC Newsnight the Unite trade union has decided to cut its funding of Labour by 10 percent as they’re “just not listening”.
Len McCluskey, Unite’s general secretary, warned there could be more cuts to follow.
Explaining his opposition to the security bill Mr Corbyn tweeted: “I have grave concerns regarding the Covert Human Intelligence Sources Bill.
“It could enable unnecessary and unlawful interference with the legitimate activities of trade unions, environmentalists, anti-racists & other campaigners.
“We must always stand up for human rights.”