Sen. Alan K. Simpson (R-Wyo.) was told yesterday that he will have to resign as chairman of the Senate Veterans' Affairs Committee because Republican Party rules prohibit a GOP Senate majority whip from chairing a standing committee.

Simpson was selected by Senate Republicans last week to be the majority whip in the 99th Congress that convenes next month.

Simpson spokesman Donald L. Hardy said the ruling shocked Simpson because he had planned to retain his chairmanship. "The senator has asked our staff to investigate the rules, but it is our understanding that he will have to give up the committee chairmanship," Hardy said.

Sens. Strom Thurmond (R-S.C.) and Robert T. Stafford (R-Vt.) are next in line for the chairmanship, but both chair Senate committees and are expected to pass it on to Sen. Frank H. Murkowski (R-Alaska).

Murkowski was in Taiwan yesterday holding hearings as chairman of the Senate Foreign Relations subcommittee on east Asian and Pacific affairs, an assignment that has received most of his attention during his first term.

Simpson's chief committee counsel, Anthony J. Principi, had said Simpson would continue as chairman, based on a precedent set by Sen. Alan Cranston (D-Calif.), the committee's ranking minority member, who held both jobs when the Democrats controlled the Senate between 1977 and 1980.

Hardy said Simpson received a telephone call yesterday from Republican officials, who told him that party rules prohibited him from holding both positions.

Simpson has been regarded as an active committee chairman. He recently helped to negotiate a compromise Agent Orange compensation bill that brought together veterans' groups, which claim the herbicide harmed Vietnam veterans' health, and the Reagan administration, which contends there is insufficient evidence that the defoliant injured soldiers who were exposed to it.