Staff at the organisation aimed at tackling online child sexual exploitation have to share computers and youngsters could be put at risk because of problems at the body, ex-employees have claimed.
One ex-member of the Child Exploitation and Online Protection Centre (Ceop) claimed that staff were "fighting to do their job".
But the National Crime Agency (NCA), of which Ceop has been part since last year, said the centre was "stronger and more resilient" than when it was a standalone body.
Former Ceop social worker Emma Howard, who left in May, said social work at the centre "became very very difficult because it didn't fit into a traditional law enforcement approach".
She told BBC2's Newsnight: "It was seen as peripheral, it wasn't valued. Senior managers within the social work team, within the child protection team at Ceop, were fighting to be able to do our job before we could even get on and do our job."
Setting out her concerns about the IT at Ceop, she said: "There are people at Ceop who don't have direct access to the internet. They have to share that access with other people at Ceop."
She added: "If government continues to underfund services like Ceop then these children will continue to be at risk because the resources aren't there to protect them."
Former detective Tom Simmons, who retired earlier this year, told the programme: "Clearly we are leaving children at risk of sexual abuse, and we've just seen in the press the historic abuse cases, things from many, many years ago that are still causing so much hurt and so much pain to people.
"Do we want to be in a position in 15 years time when we look back and say, yeah, we had all those investigations where we didn't do anything or we could have investigated and we've left all those abusers out there to abuse?"
Former Ceop chief executive Jim Gamble, who quit in 2010 after the plan to make the organisation part of the NCA was announced, told Newsnight: "I don't accept that it hasn't changed for the worst. Ceop was about being child centred.
"Ceop was an organisation where child protection wasn't part of the agenda, it was the agenda; where we blended social care with education and a professional criminal justice response.
"I believe that's been lost."
He added: "At best it has really withered on the vine and at worst now we have a situation where too few specialist staff are given far too much work to do. We know mistakes have been made and now we have the National Crime Agency saying things are much better. How can that be?"
The NCA, which was formed in October last year, insisted Ceop was better resourced as a result of the change and tackling child sexual exploitation was a "key priority".
A spokesman said: "Ceop is stronger and more resilient for being part of the NCA, where it benefits from increased overall resources dedicated to tackling child sexual exploitation, and greater operational reach.
"Within the NCA, the Ceop Command also has access to a range of other specialists, including those in the National Cyber Crime Unit, investigation teams, and the NCA's international network.
"Combating child sexual exploitation is a key priority for the NCA, and it is only by utilising the full range of skills and expertise at our disposal that we can have the biggest impact against perpetrators, and be of most value to children."
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