Varoufakis made the claim in a leaked conference call with London investors, during which he said he had been secretly building a parallel money system that involved hacking into his ministry's computers because they were controlled by the creditors.
"On what Mr Varoufakis has been saying, the allegations that the troika was controlling the secretariat general of public revenues are false and unfounded," European Commission spokeswoman Mina Andreeva told a news briefing, referring to the creditor "troika" of the Commission, European Central Bank and International Monetary Fund.
"The Commission and IMF only provide technical assistance to the tax administration but certainly do not control (the agency)," she added. "Alleging that the troika would be controlling the secretariat... Is simply not true."
The controversial Varoufakis resigned the day after Greeks voted against creditor bailout terms in a referendum on July 5. The government later accepted even harsher terms in a deal at an all-night eurozone summit on July 12-13.
In a series of shock revelations, former economics professor Varoufakis told investors he had been secretly planning for a parallel system of liquidity that could allow a Greek exit from the euro "at a drop of hat".
"It was not under control of my ministry... It was controlled by Brussels. The general secretariat is appointed, effectively, through a process that is troika-controlled and the whole mechanism within," he said.
The revelations involving Varoufakis overshadowed the start of work in Athens between the Greek government and its international creditors on launching a third bailout programme for Greece by mid-August.
"It is important not to look into the past, but the future," she said.
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