The pro-Kremlin group “Killnet” has claimed responsibility for the attack.
Several public and private websites in Lithuania were temporarily hit by a concerted cyberattack on Monday, authorities say.
According to Jonas Skardinskas, director of the National Cyber Security Centre, the attacks "probably" originated in Russia and have already been "contained".
The pro-Kremlin group Killnet has claimed responsibility in a video on their Telegram account.
The incident comes just a week after Kremlin officials threatened to retaliate because Lithuania restricted the transit of steel and ferrous metals to Russia's exclave Kaliningrad in accordance with EU sanctions.
"The attack will continue until Lithuania lifts the blockade," a Killnet spokesperson said.
The ban on goods to Kaliningrad had prompted a flurry of angry retorts from the Kremlin, which denounced the move as unprecedented and unlawful.
Local authorities in Lithuania had warned that cyberattacks were likely to follow after Moscow threatened a "non-diplomatic" response.
According to the Internet monitoring observatory Netblocks, the cyber attack was a distributed-denial-of-service (DDOS) attack, which affected "secure networks used by state institutions".
In a DDOS attack, a website is flooded with messages or connection requests in an attempt to shut it down.
The Lithuanian State Tax Inspectorate and Migration Department were among the public institutions and companies that were forced to suspend online services for several hours.
"It is very likely that attacks of similar or higher intensity will continue in the coming days, especially in the transport, energy and financial sectors," Skardinskas said.
Lithuanian Prime Minister Ingrida Šimonytė has also noted that cyber-attacks had been recurring since Russia's invasion of Ukraine in early February.