Dmitry Shlyakhtin, the president of the Russian track and field federation, has resigned two days after he was accused of obstructing an anti-doping investigation using fake medical documents.

Shlyakhtin told an emergency federation conference in Moscow that he is stepping down. He was already provisionally suspended pending a full hearing on the charges from the Athletics Integrity Unit.

Shlyakhtin took office in January 2016 pledging to overturn Russia’s suspension from international track events due to widespread doping. Nearly four years later the suspension is still in place.

On Friday night, the chances of the Russian flag flying at next year’s Olympics had taken a potentially lethal hit when anti-doping regulators recommended the country be declared noncompliant for tampering with data that was supposed to help bring the entire cheating episode to a close.

The World Anti-Doping Agency announced its compliance and review committee delivered the recommendation to the agency’s executive committee, which will discuss it on 9 December. If the executive committee agrees to declare Russia’s anti-doping agency, Rusada, noncompliant, it will set in motion a process that could end with Russia being barred from the Tokyo Games.

This marks the latest chapter in a scandal that began before the 2014 Sochi Games, when Russian officials designed a scheme to allow their athletes to dope without getting caught by substituting urine samples taken after competition with clean ones stored earlier.

Under rules written in the aftermath of that scheme, the Russians could appeal any sanction to the court of arbitration for sport. The International Olympic Committee would have to abide by the decisions from Wada or the court, though its president, Thomas Bach, said earlier this week he was not in favour of a total ban.

Dmitry Shlyakhtin speaks to the media in Russia on Saturday. Photograph: Kirill Kudryavtsev/AFP via Getty Images

Muddling the case even more are a pair of duelling rulebooks – one in effect now, the other supposed to go into effect in 2021. The current rules offer no leeway in the case of a “critical” violation, of the kind confronting Russia. They read: “The athletes ... representing that country ... will be excluded from participation in or attendance at the Olympic Games ... for the next edition of that event, or until reinstatement (whichever is longer).”

The rules scheduled to go into effect in 2021, however, say athletes “may” be excluded from major events “other than the Olympic Games”.

At the last Winter Games, the IOC banned Russia as a country but allowed 168 Russian athletes to compete under the banner “Olympic Athlete from Russia”. A similar arrangement may be made for Tokyo.

That news, delivered late on Friday, came hours after track’s governing body said it was reviewing whether to continue with such an arrangement in that sport after new charges that senior officials in the country’s track federation faked medical records.

World Athletics – formerly the IAAF – is also considering stripping Russia of its membership. Sebastian Coe, the World Athletics president, said: “We need to deal with renegade factions like this.”

Lord Coe added that the charges and suspensions against Russian officials were so wide-ranging that they left the task force with almost no one left to talk to.

One route could be to close the Russian track federation and set up a new national governing body. Shlyakhtin and four other senior officials are accused of obstructing the investigation into the 2017 world championship silver medallist Danil Lysenko, who was accused last year of failing to make himself available for drug testing.

Russian high jumper Danil Lysenko at the 2018 IAAF World Indoor Athletics Championships. Photograph: Ben Stansall/AFP via Getty Images

The high jumper allegedly provided fake medical documents as an alibi with help from the officials. He and his coach have also been suspended by the Athletics Integrity Unit pending full disciplinary hearings.

The three-times women’s world high jump champion Mariya Lasitskene assailed Russian track leaders after they were charged on Thursday, saying they have made a doping nightmare even worse. Lasitskene called for swift and radical reforms, and the removal of officials appointed by Shlyakhtin.

In the Wada case, the sanction would be directed at Russia’s anti-doping agency, which has been revamped in the wake of a scandal that investigators showed was directed by government authorities.

Rusada’s current leader, Yuri Ganus, has been bracing for such a decision and urging his own government to come clean, and help stamp out the embers of a scandal that has gone on for five years and now threatens an entirely new generation of athletes.

Wada lifted Rusada’s earlier suspension as part of an agreement that it would receive the data, only to later discover it had been tampered with, and that the tampering did not appear random. Wada said it had built more than 40 cases based on data that had not been tampered with, and corroborated information brought to the agency via whistleblowers who unearthed the case.