The empty Ectophial was obtained by emptying the ectophial, which teleports the user to Port Phasmatys. The ectophial would get automatically refilled at the Ectofuntus.
An update on 10 February 2009 added a feature wherein the Ectophial automatically refills itself after arriving at the Ectofuntus. Before the update, the Ectophial had to be manually refilled. Players who wished to leave their Ectophial empty could simply walk away from the Ectofuntus immediately upon arrival in order to interrupt the automatically triggered refilling, or do one of the following: clean a herb, drop one or more items, eat something, teleport from Ape Atoll while wielding a greegree or get frozen immediately upon arrival. You can still obtain an empty ectophial by using the ectophial to teleport, then immediately start worshipping the Ectofuntus, switching weapons immediately, digging a spade rapidly during and after the teleport, or losing connection (disconnecting). Quickly moving away by pre-selecting a point to walk to as you are teleporting in also prevents the character from filling the ectophial upon arrival.
An update on 30 April 2018 made it so the Ectophial doesn't empty itself upon teleporting, rendering the empty version unobtainable.