Three-phase circuits require additional conductor combinations to be tested. As well as the standard all-live-to-earth and live-to-live tests, you must test between each phase combination.
The full set of tests for a three-phase, four-wire circuit is: L1+L2+L3+N to E (all live conductors to earth), L1 to L2, L1 to L3, L2 to L3, L1 to N, L2 to N, L3 to N. All readings must be at least 1.0 MΩ. In practice, many electricians use the "all connected together" method — connect all live conductors together and test to earth in one go, then separate them and test between each pair. The first test confirms the cable-to-earth insulation; the individual tests confirm the inter-conductor insulation.
For three-phase motors, the motor windings themselves have their own insulation resistance that is tested separately from the cable. Motor winding IR testing is beyond the scope of standard BS 7671 testing and is covered by BS EN 60034-1. However, if a three-phase circuit feeding a motor produces a low IR reading, disconnecting the motor and re-testing will clarify whether the problem is in the cable or the motor.
For more on testing three-phase installations, see our dedicated three-phase testing guide.