Is the salary a doctor receives considered lawful (halal) or unlawful (haram) if the prevailing custom in the ministry regarding attendance is to be present two or three days a week instead of six days, with the knowledge of officials, and does this custom remove the sin from him?

As long as your contract with the Ministry stipulates your presence six days a week, you must adhere to that and receive salary commensurate with your attendance. The prevailing custom between you and the doctors does not exempt you from attendance. Likewise, the permission of the hospital director does not exempt you from attendance unless he is authorized by the Ministry to permit employees to be absent.