Alexander Petrov, Storchak's defence lawyer, said: "He gave testimony but did not admit any guilt."
After the hearing at Moscow's Lefortovo jail, Petrov said the minister would probably appeal against the charges.
Analysts say the case, which is related to debts owed by Algeria, may be a political attack on Kudrin.
Kurdin was promoted in a recent cabinet reshuffle in which allies were also appointed to key posts.
There is speculation in the media that the investigation could have a political element amid uncertainty about the future of Vladimir Putin, the Russian president.
Storchak was arrested along with two other suspects, Vadim Volkov, president of Moscow's Interregional Investment Bank and Viktor Zakharov, head of a company called Sodexim.
According to the finance ministry, in 1996 Sodexim was selected as an agent to collect a $26 million debt owed by Algeria in a trade deal.
After Algeria failed to deliver the promised goods, Sodexim turned to the government to seek repayment of the debt along with interest.
The ministry said this was part of a wider debt restructuring deal between Russia and Algeria.
Kudrin has expressed dismay at the arrest of Storchak.
After being appointed deputy finance minister in 2005, Storchak negotiated the early repayment of $22.5 billion in debts to the Paris Club of creditor nations last year.
The Paris Club is a group of financial officials from 19 of the world's richest countries that provide financial services such as debt relief to indebted countries and their creditors.