The resignation of the head of child protection is proof an independent inquiry into the Northern Territory's abuse "crisis" is desperately needed, the opposition says.

Jenny Scott, who led the territory's child protection and family services reform agenda, quit her role as executive director of the NT Department of Families and Children earlier this week.

Her resignation, which was confirmed on Friday by a spokesman for the department, comes just one week after the NT government faced intense scrutiny over its handling of a series of child abuse cases.

"The minister can no longer ignore the overwhelming evidence that child protection is in crisis and must be subject to proper scrutiny before undergoing fundamental reform," Opposition child protection spokeswoman, Jodeen Carney said in a statement.

The NT Department of Health and Families has been accused of failing to investigate warnings the children involved in a recent spate of abuse and neglect cases were at risk.

While the Henderson Government has committed to undertaking two separate investigations into the territory's child protection system, Ms Carney says that is not enough.

"It is no surprise the system is in crisis given the number of child abuse notifications is increasing exponentially whilst the number of child protection workers remains virtually stagnant," she said.

"I've no doubt an independent inquiry will reveal enormous pressures within the child protection system in the Northern Territory.

"I note both the Australian Medical Association and Bravehearts want the minister to abandon her planned internal inquiry.

"Rather than making veiled threats to public servants who courageously come forward to expose deep seated failings within the child protection system the minister should be encouraging them to testify before a fully independent inquiry."