Mr McDonnell said the former shadow foreign secretary has a “fantastic role” to play in Labour’s future but ruled out any attempt to prevent Mr Benn’s deselection.
The Yorkshire Post reported earlier this month that backers of Labour leader Jeremy Corbyn had seized control of the Leeds Central constituency Labour party.
Mr Benn has become a hate figure for a section of Corbyn supporters who blame him for triggering the sequence of events which led to the Labour leader facing a challenge over the summer.
Mr Corbyn saw off the challenge from Pontypridd MP Owen Smith and despite public calls from the Labour leader for the party to unite some of his supporters have voiced a desire for revenge against senior figures who failed to back him.
Sitting Labour MPs do not currently face mandatory reselection although some around Mr Corbyn would like the measure reintroduced as a way of targeting his critics.
But there are other party mechanisms which could be exploited to remove a sitting MP and there are fears among allies of Mr Benn that the election of supporters of Mr Corbyn to committee roles in his local party could be the first step in an attempt to unseat him.
Asked about the Leeds Central MP, Mr McDonnell told BBC Radio Five Live’s Pienaar’s Politics: “Labour leadership doesn’t involve itself in local selections to the local party.
“I think Hilary Benn’s got a fantastic role to play.
“He’s a friend of mine and I hope he continues to play a role in our party at whatever level.
“But we can’t interfere in local democracy in our party. We’re a democratic party.”
Mr McDonnell also said reselection battles were inevitable in constituencies facing boundary changes.
In the aftermath of Mr Corbyn’s re-election as Labour leader, Mr Benn called on the party to “face outward” and to “give the British people a sense of hope about the future”.
All Labour MPs face a “trigger ballot” of local branches and affiliated organisations between elections which is normally seen as a formality but could be used as a deselection mechanism.