The court upheld investigators' request to keep Storchak, a key figure in Russia's foreign debt talks, in pre-trial detention until July 9. His custody has thus been extended to a total of about eight months.
"The court reached a conclusion that the investigators' request should be met, and that a release is impossible," presiding judge Andrei Rasnovsky said, adding that if left at large the suspect may flee or pressurize witnesses.
The court earlier turned down an appeal by Storchak's lawyers asking the court to release him from custody until his trial begins. Finance Minister Alexei Kudrin and three members of the State Duma, the lower house of parliament, earlier offered personal guarantees to secure his release.
Investigators said they needed three more months to complete the probe, due to its complexity.
A lawyer acting for Storchak said the defense team would appeal against the decision with the higher Moscow City Court within 10 days.
The deputy minister was arrested on November 15 last year. He faces five to ten years in prison if convicted. He has denied all charges against him.
The case against Storchak has triggered speculation over attacks on the Kremlin's liberal bloc and has revealed divisions in the Prosecutor General's Office and its main investigative committee, which has pushed for Storchak's prosecution. Top prosecutors have rejected fresh charges against Storchak.
The finance minister and now also first deputy prime minister, Kudrin, said on Tuesday he was surprised by the court decision, and that he was still ready to guarantee Storchak would not escape or hinder the investigation.
"My guarantees for Sergei Anatolyevich remain in place," Kudrin said. "I guarantee that if he is freed on bail or a written pledge not to leave the city, or if he is placed under house arrest, he will not flee, but will cooperate with investigators as a loyal citizen."
"The reasons offered for his prolonged detention that he might intimidate, pressurize witnesses or destroy evidence are beneath any criticism," Kudrin said, reiterating that Storchak had not been involved in any illegal activities.
Investigators earlier said Storchak's arrest was related to the settlement of Soviet-era debts.