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Following June 4, 1989, the PAP saw its status rising. However, on February 2, 1996, the murder of Li Peiyao (李沛瑤), a vice-chairman of the National People's Congress, by a PAP soldier led to a wide reshuffling in the PAP leadership. Ba Zhongtan (巴忠倓), the PAP Commander, resigned "because of his age" (he was born in 1930). So did Zhang Shutian (張樹田), the Political Commissar, as well as other leading PAP officers. Ba Zhongtan was widely rumored to have been involved in several scandals at that time. His close connection with Jiang Zemin probably helped him, and he was nevertheless elected as an army representative in the Ninth NPC (in 1993 he was elected as a Shandong representative to the Eighth NPC).

With a new leadership, the PAP's political status continued to rise. At the Fifteenth Party Congress (in September 1997), the PAP had 37 representatives which had been elected by an independent electoral college, while in the past they were amalgamated with the PLA. The PAP Commander, Yang Guoping and the PAP Political Commissar, Xu Yongqing (徐永清) were made members of the Central Committee (CC), a position which had not been given to their predecessors. Besides, a PAP Deputy Commander, Lieutenant General Zhu Chengyou (朱成友), a Deputy Commander of the Chendu Military Region until December 1996, became an alternate CC member, thus placing him at a higher political level than most deputy commanders of the military regions.

In another development, on August 1, 1996, a PAP Military Court and a PAP Military Procuratorate were set up and ranked as organizations of "large military unit level" (大單位級). In other words, the PAP can be considered to be now at the same level as the military regions. This was also underscored, on March 27 this year, when Commander Yang Guoping became the first three-star general in the PAP's history.