Lysenko was provisionally suspended last August on the eve of the European Championships in Berlin, after failing to make himself available for out-of-competition drug testing.
According to the Sunday Times, Russian athletics federation (RUSAF) officials fabricated documents to show the 2017 world silver medallist was too ill to provide his whereabouts.
The newspaper claimed these documents came from fake doctors working at a bogus clinic in Moscow.
"The address used is a real address where there is a demolished building," Russian Athletics Federation spokeswoman Natalia Yukhareva told AFP.
She denounced an "information war," which, she said was "not only related to athletics."
"The Sunday Times article is indulging in wishful thinking," Yukhareva said.
The AIU, a watchdog founded by athletics' governing body to combat doping in the sport, confirmed on Sunday that it was looking into "a matter relating to the explanation provided by a Russian athlete in defence of a whereabouts violation in 2018".
Yukhareva said the Russian Federation would "fully cooperate" with the AIU.
"We are waiting for the results" of the investigation, she said, adding that until then, "making comments would be inappropriate and prohibited by the anti-doping regulations".
She also asked why the revelations came just before the IAAF Council meeting in Monaco on 8 and 9 June.
In an email sent Sunday to AFP, the IAAF said its taskforce "will prepare a report on all relevant matters and a recommendation for the IAAF Council, which will meet in Monaco on June 8 and 9."
Global athletics chiefs banned Russia in November 2015 because of evidence of state-sponsored doping, but Russian athletes cleared by the IAAF can compete as neutrals.
At the 2016 Olympics in Rio, US-based long jumper Darya Klishina was the only Russian athlete cleared to participate.
Last year Lysenko, the world indoor champion, had been one of 74 athletes allowed to compete under a neutral flag before losing his status.