Revd Helen Hayes held Holy Communion outside Church House in Westminster, which is hosting the event with businesses like Airbus - a company which makes civilian and military aircraft.
The Land Warfare Conference is expected to explore defence policy following last week's decision to leave the EU and was organised by the Royal United Services Institute.
Defence Secretary Michael Fallon will also address the event tomorrow.
Currently, the Church of England does not invest in companies which derive more than 10% of their profits from weapons.
According to the Fellowship of Reconciliation group, over 3,000 people have so far signed a petition calling on Church House not to host events sponsored by arms companies.
Revd Helen Hayes, from the Fellowship, said: "We are here today to reflect on the arms trade and to pray for its victims - for sisters and brothers suffering the violence of conflict and war, human rights abuses, homelessness and hunger.
"Jesus died on a cross because he refused to stop speaking out for the poor and oppressed. He refused to stop speaking out for those with no voice, for those with no power.
"The victims of war need the church's voice to stand 'with' them, stand 'for' them, not collude with those who stand in the corridors of power and further enable them to oppress the weak and the vulnerable."
A Church of England spokesman said: "The Church House Westminster provides a meeting space and conference facilities for a range of bodies from Government Departments to Think Tanks, from UK Feminista through to the General Synod of the Church of England.
"The Royal United Services Institute (RUSI) is a long established think tank which deals with foreign policy, defence and security.
"To suggest that by accepting this booking from the Royal United Services Institute Church House is accepting money from arms dealers or is supporting arms sales is ludicrous."
