How Japan's naval chief could bring down a government

Was Japan's navy minister subordinate to the chief of the naval staff?

In practice, yes: the staff chief could force the minister's resignation and thereby bring down the government.

The navy minister was usually senior in ordinary terms but still junior among Japan's leading admirals. The chief of the naval staff could order the minister to resign. Because a serving officer was required for the ministry, that resignation could collapse the government. This institutional power helps explain why senior admirals mattered to Japanese politics far beyond fleet operations.