The commission acted after a complaint from Jewish Human Rights Watch in July.
John Hilary, War on Want executive director, confirmed that the charity had been asked for further information.
“We have received a letter from the Charity Commission saying that they have received this complaint from the so-called Jewish Human Rights Watch,” he said.
“We have been asked questions by the commission relating to this complaint.”
In a statement issued on Wednesday, a JHRW spokesman claimed War on Want was being investigated.
The statement said: “Our complaint to the commission in July pointed out that for too long War on Want has demonstrated a troubling obsession with protesting against the Jewish state instead of attending to its ostensible charitable goal of fighting poverty.”
