Mooney, a British communications and learning specialist with a Non-Governmental Organisation (NGO), was killed along with an indigenous training assistant, Matthew Oguche.
Three other aid workers were also abducted in an attack coordinated by gunmen at Kujuru resort.
Kallon condoled with the deceased’s family in a statement issued on Monday in Maiduguri by Smantha Newport, Communication Analyst, UN Office for Coordination of Humanitarian Affairs (OCHA).
He said: “I express my deepest sympathies to the families, colleagues and friends of these brave and dedicated aid workers, who were selflessly committed to humanitarian work in Nigeria.
“This horrific tragedy has left the entire humanitarian community in mourning.”
According to the statement, Mooney has been working in Nigeria for nearly two years, and known for her devotion in countering hate speech and violence.
It added that Oguche was providing training to partners in personal safety and hostile environment awareness.