The International Association of Athletics Federations council met in Vienna to discuss lifting the suspension, but made a "unanimous" decision that Russia had not met its requirements in tackling the country's doping problem.
"Although significant progress has been made, several important criteria were not satisfied," Rune Andersen, head of the IAAF's independent task force, told reporters.
"The deep-seated culture of tolerance of doping appears not to have been changed materially. The head coach of Russian athletics and many athletes appear unwilling to acknowledge extent of the doping problem and ignore the anti-doping rules."
The Norwegian's task force also found that Russia has still not created "a strong and effective anti-doping infrastructure capable of detecting and deterring doping."
It also reported that Russian authorities had "orchestrated systematic doping and the covering up of adverse analytical findings."
The International Olympic Committee (IOC) will meet next Tuesday to decide whether to uphold the IAAF's decision, which will determine if Russia's track and field team can compete in Rio in August.
"We now appeal to the members of the (IOC) to not only consider the impact that our athletes' exclusion will have on their dreams and the people of Russia, but also that the Olympics themselves will be diminished by their absence," said the Russian Ministry of Sport, which added that it was "extremely disappointed by the IAAF ruling.
IAAF president Sebastian Coe said the decision was made "in the best interests of the sport."
"We have to make sure that for generations to come, that athletes are competing, the public have confidence in what they're watching, and that we have athletes in safe and secure systems," Britain's two-time Olympic gold medalist told CNN's Amanda Davies in Vienna.
The IAAF said it has brought in a new rule which will allow Russian athletes who have been training in other countries under more rigorous anti-doping regimes to appeal to compete at the Olympics as independent entries.
"It is possible that there are athletes who are not tainted under the Russian system ... the doping review board will make an assessment," Coe told reporters.
Andersen said any Russian athlete who has made an "extraordinary effort" to fight doping -- such as whistleblower Yulia Stepanova
-- could also apply to compete as an independent.
Before the decision was officially announced by the IAAF, Russian news agency Tass published quotes from athletes unhappy with the ruling, following earlier confirmation by Russian athletics' secretary general Mikhail Butov.
"I am in shock," javelin thrower Very Rebrik told Tass. "I will keep getting ready for the Olympics until the very end, no matter what happens, as I am not involved in all of these scandals."
"This is an unfair decision," triple jumper Yekaterina Koneva told Tass. "The big question is why they are doing this to Russia."
Pole vaulter Yelena Isinbayeva, who won Olympic gold in 2004 and 2008, went even further, saying: "This is a violation of human rights. I will not be silent. I will take measures."
Russian President Vladimir Putin said before the announcement that "there can't be a collective responsibility for all the athletes or the athletes of a certain federation, if certain individuals have been found using doping. The entire team should not be responsible for those who committed the violation."
Speaking later at the St. Petersburg International Economic Forum, Putin added: "Let me emphasize that we have never supported any violations in sports.
"We have never supported that at the state level. And we will never support this. We will never support any doping or any other violations in this area. And we are going to cooperate with all the international organizations in this regard."
The IAAF issued a provisional ban against Russian track and field athletes from international competition in November on the heels of an explosive report by the World Anti-Doping Agency that detailed what the agency said was widespread doping in Russian athletics.
The report detailed a "deeply rooted culture of cheating at all levels" of Russian athletics and implicated athletes, coaches, doctors, laboratory personnel and government officials.
On Wednesday, WADA released a new report
detailing what it said were Russian efforts to obstruct testing, including intimidation from armed federal security agents.
It said Friday it "fully supports" the IAAF decision and is now awaiting the results of its own independent report, which it hopes to release within five days of its submission on July 15.
"It is clear there is a serious need for culture change in Russia within government and among sports leaders, athletes and athlete support personnel," WADA president Craig Reedie said in a statement.