His All Black appearances as a starter were somewhat irregular thereafter, as Andrew Mehrtens was generally preferred as the first-choice flyhalf for the side during the period from 1995–2002. He was selected for the 1999 All Blacks World Cup squad but became injured in training at London, so did not play a match in that tournament. However, following an exceptional season for the Blues in Super 12, Spencer became first-choice first five-eighth for the All Blacks in 2003, and was a part of the squad for the Rugby World Cup that year.