The shadow chancellor said Mr Benn has an “important role” to play in any future Labour administration.
But amid reports Mr Benn is among those shadow cabinet members whose role is under threat, Mr McDonnell would only say Labour leader Jeremy Corbyn is responsible for the decisions if there is a reshuffle in the coming weeks.
Mr Benn’s position has come under greater scrutiny after he spoke in favour of UK military action in Syria - a stance which contradicted Mr Corbyn’s.
Appearing on BBC Radio 4’s Today programme, Mr McDonnell said: “Jeremy Corbyn is the leader of the party. If there’s to be a reshuffle, he will announce that, I’m sure, in the coming weeks.”
Told Mr Benn may like to know if he should focus on helping his constituents in Leeds with flooding rather than global issues, Mr McDonnell replied: “Hilary Benn has an important role to play in any future Labour administration.
“He’s doing a great job in his constituency at the moment, as are a large number of MPs.
“I am hoping we can assist people in their homes in an emergency way at the moment, but more importantly they want to be reassured that politicians are coming together to take expert advice and develop a long-term plan.”
Given a third attempt to clarify Mr Benn’s future, Mr McDonnell reiterated the Labour leader will determine the party’s future administration.