Mark Regev, a spokesman for the Israeli government, denied that the amended measure was aimed at expelling Palestinians, but instead, said it would safeguard their rights.
"What we've done here is we've strengthened the rights of people who face such deportation by creating ... an independent judicial oversight mechanism, which makes sure there are checks and balances and that the legal rights of people are protected," he told Al Jazeera.
Under the old order, those served with deportation orders could be deported the same day, whereas the new amendments provide a 72-hour appeal period, he said.
The controversial aspect of the measure, however, arises from the vague language now used to define an infiltrator, as reported by Israel's Haaretz newspaper on Sunday.
"The order's language is both general and ambiguous, stipulating that the term infiltrator will also be applied to Palestinian residents of Jerusalem, citizens of countries with which Israel has friendly ties [such as the United States] and Israeli citizens, whether Arab or Jewish," Haaretz said.
"All this depends on the judgement of Israel defence forces commanders in the field."
Palestinian leaders in the West Bank have condemned the policy, saying it contradicts international humanitarian law as well as UN Security Council decisions.
The measure "threatens the emptying of large areas of land from its Palestinian inhabitants," Salam Fayyad, the Palestinian prime minister, said in a statement on Monday.
"The order targets thousands of Palestinians from Gaza who work and live in the West Bank and could lead to their forced deportation to the Gaza Strip," he said.
Palestinians who have identification papers from neighbouring countries and foreign women married to Palestinians residing in the West Bank could also be affected by the changes.