109 lawmakers voted in favor of his appointment, four were against and five abstained.
Under the law, the SSD director is appointed and dismissed by the president upon the parliament's approval.
Dainius Gaizauskas, chairman of the parliamentary Committee on National Security and Defense, said earlier the SSD's activity has improved considerably under Jauniskis' leadership. Therefore, he called on lawmakers to back Jauniskis' appointment "because he's done all assigned work during his term".
"I see the huge progress (the SSD – BNS) has done and propose to allow it to continue growing," Kestutis Masiulis, a representative of the opposition conservative Homeland Union – Lithuanian Christian Democrats, said.
Meanwhile, Povilas Urbys of the non-attached group, said Jauniskis' appointment for a second term is related to politicians' wish to have more influence on intelligence institutions.
"He (Jauniskis – BNS) has to realize that serving the state is not the same as serving a person," he said.
Naglis Puteikis of the ruling Lithuanian Farmers and Greens Union's political group, said the surveillance of many people the SSD is allegedly carrying out cannot be justified. "He does not meet the Western democratic standards," the politician said.
The SSD chief said earlier the intelligence agency vetted around 80,000 people in 2019.
Lithuanian President Gitanas Nauseda nominated Jauniskis for a second term last week after the CBSD endorsed its conclusions on the SSD situation.
The committee concluded that the SSD acted lawfully when vetting people within circles of presidential candidates, but it suggested that the SSD should changes its working procedures and avoid verbal orders to vet people.
The CNSD probe came in response to a report by a high-ranking intelligence officer, who informed MP Vytautas Bakas, the former head of the CNSD, that, acting on orders from the top SSD officials, intelligence collected in 2018-2019 information about the inner circle of Gitanas Nauseda, then a presidential candidate, and on Lithuania's former foreign minister and diplomat Vygaudas Usackas.
Provided by the whistleblower, the list of people the SSD vetted includes over 60 well-known people from the areas of business, culture and entertainment.
The whistleblower said earlier he believed intelligence chief could have violated the principles of lawfulness and political neutrality with their actions.
The SSD chief said people were vetted pursuant to existing laws, adding that collected information was no provided to unauthorized people.
Jauniskis was first appointed to lead the SDD on April 13, 2015.