"On Sunday night, the orbit of the ISS was successfully corrected," Roscosmos told Russian news agencies, 48 hours after the initial attempt to switch on the spacecraft's engines proved unsuccessful.
ISS is now at the right altitude for its three crew members to return to Earth in early June after the operation by the Progress M-26M cargo vehicle, which began just after 3:30 am Moscow time (0030 GMT) and took about half an hour.
Last morning, hours after the failed first attempt to right the ISS, Russia also lost a Mexican telecommunications satellite following the failed launch of the Proton-M carrier rocket from Baikonur Cosmodrome in Kazakhstan.
Russian Prime Minister Dmitry Medvedev immediately launched an inquiry after the satellite incident, demanding answers from the head of the space agency, Igor Komarov, and suggesting heads could roll.
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"This accident is the consequence of a systematic crisis in the (space) industry," deputy prime minister in charge of the aerospace sector, Dmitry Rogozin, said in a statement, adding that a new bill on Roscosmos would be put before Russia's parliament on Tuesday.
Russia is currently reforming its space industry, but experts say years of underfunding mean there is a shortage in new-generation specialists to replace those recruited in the Soviet era.
"For 20 years, the sector has not been funded and the staff not trained," MP Valeri Gartoung, who heads the commission for the space industry in Russia's parliament, was quoted as saying by the Russian news agency Ria Novosti.
Their return has already been delayed by a month after the failure of the April mission.
The new ISS team, which was initially scheduled to take off on May 26 from the Baikonur Cosmodrome, is now due to join the station at the end of July.