A government spokesman said that Dimitris Georgakopoulos, secretary-general at the Finance Ministry in charge of tax and customs issues, left his post.
"He resigned for personal reasons," government spokesman George Petalotis told Reuters, without elaborating.
Tax collection is a weak point in Greece's efforts to reduce its deficit as part of an €110bn (£94.8bn) EU/IMF bailout to avoid bankruptcy.
The country missed its revenue targets last year and risks missing them again in 2011, the EU and the IMF said, urging the government to do more against tax dodgers.
Moody's on Monday cut Greece's rating by three notches, citing among other reasons continued flaws in Greece's tax collecting mechanism.
"Government revenues have been slow to rebound, which is in part the result of a continued weakness in tax collection mechanisms," the agency said.
Greece has rejected the agency's criticism, saying that initial targets may have been missed but tax revenues actually rose last year, despite the country's austerity-fuelled recession.