He retained his seat in the 2009 elections, having been placed second on the Shas list, and was appointed Minister of Housing and Construction in the Netanyahu government. On 2 July 2009, it was reported that Atias had called for the segregation of Israel's Arab population from Jewish Israelis, saying that achieving it was "a national duty... populations that should not mix are spreading... I don't think that it is appropriate [for them] to live together".
Atias retained his seat again in the 2013 Knesset elections, but Shas was not included in the coalition, resulting in Atias losing his ministerial post. He resigned from the Knesset in June 2014 in order to take a break from politics, and was replaced by Yoav Ben-Tzur.
He is the father of four and currently resides in Jerusalem.