They were backed by 84 lawmakers, one was against and five abstained. The changes will come into force once they are signed by President Gitanas Nauseda.
The Cabinet had asked the parliament to debate and adopt these amendments under a fast-track procedure.
Presenting the amendments, Interior Minister Agne Bilotaite said that the country's special service indicates that migrants inflows might increase further, therefore, "measures to resolve this crisis need to be swift, deterring and united".
The adopted changed will restrict the free movement of migrants who have illegally crossed into Lithuania and limit other rights of such people when the government declares an emergency situation due to a migration influx.
Human rights NGOs, however, say the amendments will in fact legitimize human rights violations and put vulnerable people in an unsafe situation. Lawyers also say the amendments might run counter to the Constitution.
A total of 1,716 illegal migrants have been detained at Lithuania's border with Belarus this year so far, more than a 20-fold increase compared to the whole of 2020.
Most of the migrants originally come from the Middle East and Africa.
A state-level emergency situation is now in Lithuania due to the growing influx of irregular migration via Belarus.
In retaliation for EU sanctions, Minsk says it is no longer stopping migrants seeking to cross into the bloc.