The order's language was ambiguous and far from defining liabilities and rights of each group of residents in the West Bank, the daily said.
Haaretz said: "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.
"All this depends on the judgement of Israel defence forces commanders in the field."
Haaretz said the new order would likely be used first against Palestinians with Gaza ID cards and the foreign spouses of Palestinians living in the territory.
It said that until now Israeli civil courts have generally prevented such expulsions but that the amended order would grant the military full jurisdiction over the matter.
Hamoked, an Israeli rights group focused on freedom of movement, called on the military to rescind the order.
"The orders do not define what Israel considers a valid permit. The vast majority of people now living in the West Bank have never been required to hold any sort of permit to be present therein," it said in a statement.
“The definition of 'infiltrator', which exposes a person to a prison term of three to seven years could, in principle, be applied to any person the military commander wishes ill, including Israeli and international citizens."
Israel seized the West Bank, including East Jerusalem, in the 1967 Six Day War. It is expected to form the main part of the Palestinians' promised future state.
The Israeli military can issue its own orders in the West Bank, but these can be overturned by the government or by Israeli courts.