The two players are Martynas Dapkus of Trakai football club and Žalgiris Vilnius goalkeeper Armantas Vitkauskas, lrytas.lt reports.
The Lithuanian Football Federation (LFF) says the two players were suspended last week.
"We have received confidential information from the Lithuanian Anti-Doping Agency. We have test results, but we are bound by confidentiality not to disclose them. We have responded to recommendations to suspend the players in question. They have been suspended as of April 14," LFF spokeswoman Vaiva Zizaitė told lrytas.lt.
The spokesman for Trakai club, Armanas Vitkauskas, has said that the amount of Meldonium detected in Dapkus' urine is very small and is below the allowed limit.
Dapkus, 23, has played one game in the Lithuanian national football team and was previously in the national U-21 team.
Vitkauskas, 27, has also played in the national team and was signed by Žalgiris in 2012.
The World Anti-Doping Agency banned Meldonium this year, but recently said that athletes will not be sanctioned if the amount of the substance in their samples does not exceed 1 microgram.
The LFF disciplinary committee is meeting on Tuesday and can revoke the two players' suspension if the amount of Meldonium in their urine is below that limit.