The Ministry of Justice is the government organization responsible for immigration control services and includes the Immigration Services Agency and eight regional Immigration Services Bureaus, seven district offices, 61 branch offices and two detention centers. The Immigration Services Agency and regional Immigration Services Bureaus are in charge of entry into and departure from Japan, residency, deportation and recognition of refugee status.

The issuance of visas is handled by Japan's Ministry of Foreign Affairs through consulates and diplomatic offices abroad.