"I condemn North Korea's test of a long-range ballistic missile, which jeopardizes security in the Indo-Pacific region, violates the UNSC resolutions, disregards the will of the int'l community," Simonyte tweeted.
"Lithuania stands in solidarity with Japan, South Korea & other partners in the region."
South Korea's military said earlier on Friday that Pyongyang had fired an intercontinental ballistic missile that landed near Japan.
Friday's launch is the latest in a series of tests conducted by North Korea, adding to growing tensions between Washington and Pyongyang, which US intelligence believes is preparing for its seventh nuclear test.
Japan says the missile may have had the range to hit the US mainland.
North Korea claims the recent wave of launches is a response to Washington's moves to strengthen its protection of regional security allies, South Korea and Japan.