The umbrella body, plus staff from tenant organisations Volunteering England, Bond and the Black Training and Enterprise Group, got caught in the crossfire when 15 protesters stormed a suite hosting a family law conference.
Protesters let off flares and smoke bombs and when the fire alarm sounded all employees, plus 122 delegates, beat a hasty retreat.
Conference organisers Children's Law UK had been tipped off that two supporters from the fathers' rights group had applied for conference accreditation under the bogus name of the Shared Parenting Federation.
When security blocked their entry, another two protesters distracted police while 30 colleagues piled out of a van and ran straight into the London building. Of the 15 that breached security, nine were arrested but later released.
A spokesman for the NCVO, whose staff were kept out of work for 30 minutes, said the organisation supported pressure groups' right to direct action.
"However, these activities must be within the law," he added.
Glyn Farrow, director of Children's Law UK, condemned the action, which disturbed a presentation by Families Need Fathers.
Fathers 4 Justice founder Matt O'Connor replied: "They say they were trying to debate fathers issues, but they have been saying that for 30 years and it doesn't wash with us."
However, Families Need Fathers spokesman Jim Parton admitted grudging admiration for Fathers 4 Justice. "Fatherhood has received incomparably more column inches this year than last, and that isn't because of us," he said. "Without their sometimes irresponsible protests I don't think this subject would be spoken about at all.
"We have tried so hard to talk rationally about the issue. It reflects badly on policy makers that it takes something like this to get them to take action. I have to say with some regret that I'm in favour of their protests, even if we are sometimes the victim of them."