In a post on his personal blog, Varoufakis said media reports had distorted the position of the new leftist-led government. The complaint made by Athens to EU foreign policy chief Federica Mogherini had been about a lack of consultation, not about the sanctions themselves, he added, Censor.NET reports citing Reuters.
The foreign ministry declined to comment.
EU foreign ministers are expected to ask the European Commission on Thursday to prepare a new round of sanctions against Russia, aimed at punishing Moscow over its support for separatist rebels in eastern Ukraine.
Varoufakis said Foreign Minister Nikos Kotzias told cabinet colleagues on Tuesday that he had heard on news bulletins that the EU had unanimously approved sanctions against Russia.
"The problem was that he, and the new Greek government, were never asked!," Varoufakis wrote in a blog post. "So, clearly, the issue was not whether our new government agrees or not with fresh sanctions on Russia. The issue is whether our view can be taken for granted without even being told of what it is!"
However, the impression that the government of Prime Minister Alexis Tsipras is at odds with the rest of Europe over the issue was reinforced by comments from Energy Minister Panagiotis Lafazanis, who said Athens was against sanctions and "had no differences with Russia".
Tsipras himself met the Russian ambassador to Athens on Monday, the day he was sworn into office.
The statements have unnerved European leaders and prompted speculation that the Greek government was leaning towards Russia while it seeks to renegotiate its bailout program with Europe. EU ministers meet on Thursday to extend the sanctions by six months.
The speaker of the European parliament Martin Schulz, who is due to meet Tsipras in Athens later on Thursday, said Greece could not at the same time seek to negotiate with Europe over its debt and strike a dissident line on Russia.
"You just cannot, on the one hand, demand from Europe to show solidarity with your own country like Mr. Tsipras does and then, as a first official step, split the joint European position," he told German television.