Kazlauskas, 53, is set to be signed for four years until the end of Rio de Janeiro Olympics in 2016.
He will replace Kęstutis Kemzūra who led the team during London Olympics, where the Lithuanian national team lost in the quarter finals and failed to make it into the top four for the first time since Lithuania's independence two decades ago.
"I have talked to Kazlauskas. Key things have been discussed, and, I think, we'll sign him for four years on Monday," Federation President Arvydas Sabonis told journalists on Wednesday.
"Jonas is one of the best specialists. He's an authority for both young and experienced players. A generation change is taking place in the national team, and he is capable of motivating and handling the existing team," he said.
"I called Kemzūra myself and thanked him for his work in the national team, and wished him success. His contract with the federation expired after the Olympics, and we are keeping good relations with as there are few good coaches in Lithuania, and perhaps he'll be back on the team after some time," Sabonis added.
Kazlauskas coached the Lithuanian national men's basketball team in 1997-2001, and the team won bronze at the Sydney Olympics. He left the national team after it failed to get into the quarterfinals of the EuroBasket 2001 in Turkey.
Kazlauskas has coached the national teams of China and Greece and led them to win the Gold Medal at the Asian Games in 2006 and the Bronze Medal at the EuroBasket 2009.
Moreover, he has coached Žalgiris Kaunas, Lietuvos Rytas, Olympiacos Piraeus (Greece) and CSKA Moscow (Russia). Coached by Kazlauskas, Žalgiris Kaunas won the Euroleague 1998.
He worked with the CSKA the last season and was named the best coach of the Russian League of 2012. But the Russian club did not extend his contract following the loss to Olympiakos in the Euroleague final.