Manolis Panagiotakis resigned a day after Greece's newly-appointed energy minister said the new conservative government will work on a plan to salvage PPC from "the verge of collapse".
Pangiotakis will remain in his post to handle "urgent matters" until his successor is appointed, the ministry said.
New Democracy won a landslide victory in Sunday's general election, promising to unblock and boost investments in Greece.
PPC is saddled with more than 2.4 billion euros of arrears from bills left unpaid during the country's debt crisis, which began in 2009.
It has about a 70pc share of the domestic retail market and has struggled to shore up its finances.
The 51pc state-owned utility also has to sell power to alternative producers at below-cost prices to help open up the retail market under a post-bailout agreement between Greece and its international lenders.