Sergei Storchak, who was supposed to accompany the finance minister on a trip to South Africa, was detained along with two businessmen late on Thursday in Moscow on suspicion of large-scale fraud. A court issued an arrest warrant on Friday.
"The evidence in the case suggests that if left at large Storchak could flee prosecution, intimidate witnesses and destroy evidence," the Investigation Committee of the Prosecutor General's Office said.
The Investigation Committee said the arrest was related to the settlement of Soviet-era debt to commercial firm Sodexim and that Storchak was arrested along with Sodexim General Director Viktor Zakharov, and the president of Moscow-based Interregional Investment Bank, Vadim Volkov.
A spokesman for the Investigative Committee said the men are suspected of setting up an organized group plotting a large-scale state budget fund fraud and may face between five and ten years in prison.
Finance Minister Alexei Kudrin earlier said he was surprised at Storchak's arrest and considered the measure against his subordinate to be excessively harsh.
A key figure in Russia's Paris Club debt talks, Storchak assumed his current post in November 2005. In 2004, when he was still head of the international finance and foreign debt department in the ministry, his deputy was arrested on graft charges.
Denis Mikhailov, who oversaw contacts with international rating agencies and western investors in the ministry, was accused of passing confidential financial information to two businessmen, and receiving a 87,000-euro car as "remuneration."
He was originally sentenced to 10 years in prison, but Russia's Supreme Court later reduced the sentence to five years.