Finance Minister Yannis Stournaras called for Stelios Stavridis to resign following a report that he had travelled on a plane belonging to a businessman who bought gambling firm Opap from the state.
Mr Stavridis had only been in the job for four months but had faced criticism for the slow pace of privatisations.
Last week Athens finalised the sale of a controlling stake in Opap.
A group of Greek and eastern European investors paid 650m euros ($866m; £554m) for the state's 33% stake in the company.
Those investors include Greek shipowner Dimitris Melissanidis, whose private jet Mr Stavridis is said to have flown on.
Olympic site
Mr Stavridis had successfully transformed the Athens Water Board before being appointed boss of the Hellenic Republic Asset Development Fund (HRADF).
The financial target for the sale of state assets this year has been set at 2.6bn euros, but it is estimated that the final figure will be 1bn euros short.
Earlier this year attempts to dispose of Depa, the national gas utility, by selling to proposed buyer Gazprom fell through in a row over Russia's domination of energy supply in Europe.
However, Mr Stavridis told the BBC last month that the sale of state assets would net a target 4.5bn euros by 2014.
One landmark asset earmarked for sale in October is the Hellinikon Metropolitan Park - the vast former Olympic site on the coast.