"The Prosecutor General's Office has now no significant claims to the Foundation's management," the statement says.
Last month, prosecutors said spending at the Skolkovo Foundation, headed by billionaire Viktor Vekselberg, became "out of control and extravagant" and that it has inappropriately spent 125 billion rubles ($3.9 billion) of government funds.
Checks found that the violations were detected in "almost all the areas" ranging from grant-issuing process, advertising to construction.
A spokesman for the Skolkovo Foundation said after checks were launched "several procedures were introduced to guarantee the transparency and effectiveness of financial decisions of the foundation."
Criminal investigations were opened into two senior Skolkovo executives in February over the alleged embezzlement of $800,000. Law enforcement officials carried out searches at the offices of the Skolkovo Foundation's top managers in April and questioned several officials, including Vekselberg.
The Skolkovo hub, a pet project of Prime Minister Dmitry Medvedev opened in 2010 during his presidency, is often labeled Russia's "Silicon Valley" and was intended to lead the country's drive to diversify and modernize its economy and increase the output of high-tech products.