The bloc also warns it could consider sanctions if there is no improvement in the crisis, in which more than half a million Rohingya Muslims have fled a military crackdown into Bangladesh since August, a situation the UN says likely amounts to ethnic cleansing.
The agreement, approved by EU ambassadors and set to be signed off at a meeting of foreign ministers on Monday, said the rapid flight of so many people "strongly indicates a deliberate action to expel a minority".
"In the light of the disproportionate use of force carried out by the security forces, the EU and its member states will suspend invitations to the commander-in-chief of the Myanmar/Burma armed forces and senior military officers and review all practical defence cooperation," the agreement says, while calling on all sides to end violence immediately.
The EU currently bans the export of arms and equipment that can be used for "internal repression", but said it "may consider additional measures" if the crisis does not improve.
The influx of refugees into poor and overpopulated Bangladesh slowed in recent weeks but appears to have picked up again, with an estimated 11,000 new arrivals on Monday.