At the same time, the president noted that asylum seekers' rights "must not be restricted more than necessary" and called on the parliament to remove the shortcomings in the law in the near future, it said in a press release.
"Adopted by the Seimas under a fast-track procedure, the law is flawed in human rights terms," Nauseda said. "However, it would now be more dangerous to have a flawed policy on irregular migration."
"At present, it is better to have such a law than to have no regulation providing for measures to deal with the emergency situation on the Lithuanian border with Belarus. This would send a completely unacceptable signal to the countries of origin of migration," he added.
In the president's opinion, the most contentious provision of the new legislation is that the decision taken by the Migration Department after examining a foreign national's appeal under a mandatory pre-trial procedure is enforced immediately, thus violating the principle of non-refoulement of the asylum-seeker, according to the press release.
The amendments also permanently deprive asylum-seekers of the right to appeal against decisions of a court of the first instance, which goes against the Constitution, it noted.
The Seimas passed the amendments during an extraordinary session last week, in response to a growing influx of irregular migrants from Belarus.
The new legislation, among other things, reduces the processing time of migrants' asylum applications and restricts some of irregular migrants' rights when the government declares a state of emergency due to a migration influx.
Non-governmental organizations say the amendments will violate human rights and put vulnerable people in danger. Lawyers also say the new legislation may run counter to the Constitution.
On Tuesday, Povilas Maciulis, Gitanas Nauseda's chief domestic policy adviser, said that the new amendments had thrown the human rights of migrants "into the bin".
He added, however, that the president was cautious about vetoing the amendments because the parliament would need to convene an extraordinary session if he did so.
Before making his decision on whether to sign the new legislation into law, Nauseda met on Tuesday with Viktorija Cmilyte-Nielsen, the speaker of the Seimas, Interior Minister Agne Bilotaite and Laurynas Kasciunas, chairman of the parliamentary Committee on National Security and Defense.
The speaker said she promised the president that the parliament would in any case review the amendments during its fall session.
"I told him that we will go back to review that law in the fall in any case and I believe that my promise might be an important argument not to veto," the speaker told journalists on Tuesday.