It includes large sections on survival techniques and warns that Russia would not hesitate to use military force against its neighbours.
Tens of thousands of copies of the 75-page guide have been distributed.
The government has also launched a telephone hotline for citizens to report anyone they suspect of being a spy.
"Every Lithuanian citizen can become a target" of spying, said Darius Jauniskis, the head of the state security department.
Russia's relations with its Baltic neighbours have deteriorated since 2014 when Russia annexed Crimea from Ukraine.
This is the third such booklet that Lithuania's ministry of defence has published since then - but this one adopts a much more serious tone than the previous two.
It includes guides to spotting Russian tanks, bullets and mines as well as surviving in the wild.
The manual includes the words: "It is most important that the civilians are aware and have a will to resist - when these elements are strong, an aggressor has difficulties in creating an environment for military invasion."
Lithuania was part of the Soviet Union. In 2004 it joined Nato. It shares a border with the Russian exclave of Kaliningrad
Nato allies plan to send more troops and equipment to the Baltic states. Lithuania, Estonia and Latvia have expressed fears of Russian invasion, and last year Lithuania announced it would re-introduce conscription for men aged 19-26.
In August, the German government was accused of scaremongering after advising citizens to stockpile food and water for use in a national emergency.
Lithuania has updated its civil defence booklet telling citizens what to do in the event of a Russian invasion.