We demonstrate, both experimentally and by computer simulation, that while the metastable face-centered cubic (fcc) phase of Ge-Sb-Te becomes amorphous under hydrostatic compression at about 15 GPa, the stable trigonal phase remains crystalline. We present evidences that the pressure-induced amorphisation phenomenon strongly depends on the concentration of vacancies included in the Ge/Sb sublattice, but is thermally insensitive. Upon higher compression, a body-centered cubic phase is obtained in both cases at around 30 GPa. Upon decompression, the amorphous phase is retained when starting with the fcc phase while the initial structure is recovered when starting with the trigonal phase. We argue that the presence of vacancies and the associated subsequent large atomic displacements lead to nanoscale phase separation and the loss of the initial structure memory in the fcc staring phase of Ge-Sb-Te. We futher compare the amorphous phase obtained via the pressure route with the melt quenched amorphous phase.