"We should seek even closer economic ties, particularly in fields of engineering, information and financial technologies, life sciences and laser industry," Skvernelis told journalists at the government on Saturday.
Abe, the head of the government of the world's third-largest economy, was in Lithuania with a business delegation.
In Skvernelis' words, the ties between Lithuania and Japan will be deepened by the cooperation format of the three Baltic states and Tokyo.
"Shared values and good will always overcome the geographic differences between us," said the Lithuanian prime minister.
Japan's prime minister said that the recent improvements of the Vilnius-Tokyo ties had triggered bigger tourist flows. Abe called for bilateral agreements on labor holidays.
Abe is Japan's first prime minister to visit Lithuania. He was in Latvia and Estonia earlier this week.
Japan's Emperor Akihito came to Lithuania almost 11 years ago.