We study the breakup of confined fluid threads at low flow rates to understand instability mechanisms. To determine the critical conditions between the earlier quasi-stable necking stage and the later unstable collapse stage, simulations and experiments are designed to operate at an extremely low flow rate. The critical mean radii at the neck centres are identified by the stop-flow method for elementary microfluidic configurations. Two distinct origins of capillary instabilities are revealed for different confinement situations. One is the gradient of capillary pressure induced by the confinements of geometry and external flow, whereas the other is the competition between the capillary pressure and internal pressure determined by the confinements.