"I don't think there was an embezzlement attempt. This can be ruled out," Alexei Kudrin told journalists.
The deputy in question, Sergei Storchak, was detained along with two businessmen late last Thursday in Moscow on suspicion of attempting to embezzle $43 million. An arrest warrant was issued the following day.
Defense lawyers for the deputy finance minister appealed on Wednesday the official's arrest.
Russia's Investigative Committee earlier said Storchak had been arrested due to prosecutors' concerns that he could destroy evidence or intimidate witnesses.
Storchak's lawyer said Wednesday that his client could be officially charged at the end of the week.
The Investigation Committee earlier said the arrest was related to the settlement of Soviet-era debts to the Sodexim company, adding that Storchak had been arrested along with Sodexim general director Viktor Zakharov and the president of the Moscow-based Interregional Investment Bank, Vadim Volkov.
A key figure in Russia's Paris Club debt talks, Storchak assumed his current post in November 2005.
