The majority opinion also struck down the amendment allowing for a year-long detention of asylum seekers. Six justices supported the decision, with three opposing.
A majority ruling – by seven justices – nullified the law which regulated the establishment and operation of the Holot detention facility, scheduled to be shut down within 90 days.
Chief Justice Asher Grunis, in the minority opinion, argued that only the section of the law which requires the asylum seekers to mark their attendance in the afternoon should have been stripped.
Human rights activists have claimed that the new law was an assault on liberty, even after they helped shape the amendments to the previous law. The High Court justices agreed with the activists, rejecting the central sections of the controversial legislation.
An expanded panel of nine High Court justices unanimously ruled in September 2013 that the amendment to the Prevention of Infiltration Law, an amendment that allows the detention of infiltrators for up to three years without trial, is unconstitutional.
According to the judges, the arrangement disproportionately harms the constitutional right to freedom set forth in the Basic Law: Human Dignity and Liberty. The amendment to the Infiltration Law was initiated by Prime Minister Benjamin Netanyahu.
Interior Minister Gideon Sa'ar then presented a legal memorandum in November 2013 to replace the previous amendment to the Prevention of Infiltration Law.
According to the new bill, whose contents were first published by Ynet, it permits the detention of asylum seekers that enter the country only after the bill passes the Knesset: "The central issue is that the amendment applies to an infiltrator that enters Israel after this particular clause comes into effect.
"Thus it will be possible to realize the meaning of the law while balancing the difficulties discussed in the verdict – to prevent the entry of new infiltrators into Israel and to prevent these infiltrators from settling down in Israel, while providing a deterrent. With this we also need to try to give a balanced solution as such that the tens of thousands of infiltrators already in Israel are not affected."
Human rights groups have insisted that the majority of the African migrants in Israel cannot be deported because of threats to their lives in their homelands of Sudan and Eritrea.
Omri Efraim contributed to this report.