Shlyakhtin, who has served as a regional sports official, was backed by Russia's Sports Minister Vitaly Mutko and elected unanimously to head the All-Russian Athletics Federation (ARAF) after two other candidates withdrew themselves from the vote.
He will serve as an "anti-crisis" head of the body for the next several months, through the Olympic Games in Rio, before another vote in September or October, Mutko told journalists ahead of the decision.
"We must solve all of these problems quickly," he said, after Mutko said he hoped to "reinstate all the powers of our athletics federation in March."
Virtually unknown outside of Russia, Shlyakhtin has been sports minister of the Samara region on the Volga river for the last three years. Before that he headed the CSKA athletics club.
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The IAAF provisionally suspended the ARAF in November and outlined strict reinstatement criteria last month, including severing ties with Russian athletics officials, officers or staff with any past involvement in doping.
Possibly due to this, ARAF secretary general Mikhail Butov withdrew his candidacy ahead of the vote Saturday. Butov had been invited for the secretary general post by ex-ARAF chief Valentin Balakhnichev, who is now banned by IAAF for life from the sports field.
Another candidate Alexander Shustov, Russia's 31-year-old veteran high-jumping athlete, also retracted his candidacy.
"We must demonstrate consistent and tough work to eradicate our problems, to ensure that our athletes make it to the Rio Olympic Games," he told journalists.
Russia is facing an uphill battle after a World Anti-Doping Agency (WADA) independent commission alleged widespread state-sanctioned corruption and doping in the country's athletics.
Over four thousand Russian athletes have been banned from international competition and sports authorities are launching reforms and making promises to get the ban lifted in time for Rio.