Netanyahu heads a coalition with only a one-seat majority in parliament, making him especially vulnerable to the demands of religious nationalists in his cabinet regarding settlements, which much of the international community opposes.
His comments came at a time of sharp criticism internationally on Israeli settlement activity in the West Bank, including from the United States and European Union.
"The government supports settlement at any time, especially now when it is under terrorist assault and is taking a courageous and determined stand in the face of terrorist attacks," Netanyahu said at the start of a cabinet meeting, according to his office.
The buildings stand near a religious site known to Jews as the Cave of the Patriarchs and to Muslims as the Ibrahimi Mosque.
Hebron is a flashpoint in the Israeli-Palestinian conflict, with several hundred Jewish settlers living in the heart of the city under heavy military guard among around 200,000 Palestinians.
Clashes and protests have regularly broken out in Hebron. A large number of the Palestinian knife, gun and car-ramming attacks that began in October have also occurred in and around the city.
But Netanyahu said that "as soon as the procedures regarding the purchase are approved, we will allow the two homes in Hebron to be populated, as indeed occurred in similar instances in the past."
"The process of checking is starting today," he said at the cabinet meeting. "We will do it as quickly as possible. If, in any case, it is not completed within a week, I will see to it that the cabinet receives a status report."
Criticising the evictions, three right-wing members of Netanyahu's coalition had threatened to not vote with the government over the issue.
