"It's obviously deeply disappointing to us."
The girl was not a resident of the accommodation where the man worked, nor was she a Salvation Army client, Lieutenant Colonel Hutson said.
It was not known how long the man worked for the charitable organisation, but there had been no other complaints made against him.
The Salvation Army would wait to see the outcome of the police inquiry before carrying out its own investigation, he said.
Police spokesman Nick Bohm said the investigation was still in its "very early stages".
"We are yet to do a formal interview with the alleged victim, but we are talking to people that know her."
The Salvation Army was fully co-operating with police inquiries, he said.
No charges had yet been laid.
