Čiukšys and Puslys are also suspected of unlawful possession of radioactive substances.
The Special Investigation Service said the case would go to court after the suspects study the investigation materials.
The Energy Ministry, which the NPP reports to, has provided no comment on the situation so far.
Panevėžys prosecutor Dalia Markauskienė who was in charge of the investigation said the probe was not only extensive but also very complicated, as it focused on corruption allegations of top-level N-plant executives and businessmen in a company of strategic importance to national security.
"It is a large-scale investigation, the case materials consist of more than 30 volumes of documents," Markauskienė said in a press release.
The Competition Council's probe revealed that the companies involved in the auction to sell radioactive copper ferrous scrap , including Germany's Sypra and Norvesta, a Raseiniai company that went bankrupt earlier this year, had formed a cartel and were Wednesday imposed respective fines of 27,100 euros and 27,500 euros.
Lithuania's law-enforcement had suspicions about the 2014 auction to sell 2,000 tons of radioactively contaminated copper tubes, whose winner was a possibly pre-selected company, Sypra.
Janulevičius has been serving as the Ignalina facility's CEO since early March of 2013 after heading a bankrupt investment company Hermis Capital. Čiukšys, a former diplomat, headed the company between March of 2010 and April of 2011.
Abuse of office is punishable by fine or up to seven years in prison, while unlawful possession of radioactive substances is punishable by arrest or up to four years in prison.