Bishop Christopher Hill was speaking after at least 31 people were killed in coordinated attacks in the Belgian city this morning.
A suicide bomber struck first near the American Airlines desk at Brussels airport and later there was an explosion on the Metro was near European Union buildings and the US embassy.
The President of The Conference of European Churches, based in Brussels, told Premier's News Hour churches will stay open to meet their purpose, but security will be tight.
He said: "Churches are of course traditionally open and I'm sure that they will be open - a place that people will want to go - perhaps to sit in stunned silence, perhaps to ask God 'why?' and that's often a question that God doesn't get an immediate answer to that."
Bishop Christopher Hill went on: "Well I know that the Holy Trinity, which is one of the Church of England, or Anglican churches there, will not be locked - but they'll have to be vigilance and extra security measures."
Tuesday has been described as a black moment by Belgium's prime minister, Charles Michel.
David Cameron has said the countries of Europe need to stand together to make sure "appalling terrorists" "can never win".
Rt Revd Robert Innes, Anglican Bishop for Europe, described the mood on Premier's News Hour.
He said: "Things are very quiet - there's nobody around on the street, our offices are very quiet.
"We've heard the helicopter overhead for the last few hours and there are sirens in the street and so on - but we're feeling very sombre."
Downing Street said one British national is known to have been injured at the airport.
Responding to the attacks, French Prime Minister Manuel Valls said: "We are at war. In Europe we have been subjected to acts of war for several months."
Jonathan Arnott, Christian and UKIP MEP for the North East, told Premier's News Hour security has been stepped up in Brussels but questions will be asked as to why this happened.
"The big question is - what's happening in terms of intelligence, how that intelligence is being communicated to Belgian police, and there certainly are issues there - as the dust settles on this one I think there will be some serious questions."
"The major battle really is down to intelligence and security services and that's where I think we certainty need to take a good look to see if we are doing everything that we need to do."
Listen to Premier's Antony Bushfield speak to Bishop Christopher Hill here:
Listen to Premier's Antony Bushfield speak to Rt Revd Robert Innes here:
Listen to Premier's Antony Bushfield speak to Jonathan Arnott here: