The case is the latest in a string of interactions between the humanitarian charity and the commission in the past few years, all prompted by complaints that the commission said were focused in particular on the charity’s campaigning and political activities.
But John Hilary, executive director of War on Want, said the charity had followed commission guidance and the complaints were an attack by those who did not agree with the charity’s views.
He said: "Over the years, various Zionist groups have tried to use the Charity Commission’s complaints procedure to attack War on Want over its work for human rights in Palestine.
"War on Want has an ongoing relationship with the Charity Commission, like most charities do, and we are happy to comply with the commission's guidance on campaigning and political activity."
It is not known what caused the current case, but in the past month the charity has been the focus of a news story in The Sunday Telegraph, which erroneously claimed that the Department for International Development had withdrawn funding from the charity after secret recordings allegedly showed antisemitic comments being made at a rally the charity was involved with.
The paper later removed this claim from its story after the charity complained and DfID confirmed it had not been funding War on Want at the time the comments were allegedly made.
The charity, which has campaigned on issues relating to Palestinian human rights, also refuted the allegations of antisemitism.
A commission spokesman said: "The commission has received some complaints about the charity in recent years, particularly in respect of its campaigning and political activities.
"We have engaged with the charity about these issues as and when they arise and continue to do so. We intend to publish an operational case report to explain our current engagement and conclusions when we close our case."
It is not known when the case will be closed or when the report will be released.
Hilary said: "It is vital that charities like ours retain the right to engage in campaigning in furtherance of our charitable objectives, and the Charity Commission has long valued this.
"Any move to undermine that right would represent a serious attack on civil society’s ability to hold governments to account."