In a statement Wednesday, Yunus said a "great global iconic institution" was being brutalized by the government.
"Grameen Bank was created as a bank owned by poor women, and managed by poor women. Its legal structure did not allow any government interference of any kind, except for regulatory oversight," he said.
Finance Minister A.M.A. Muhith has pledged that Grameen would be better run in the absence of Yunus.
The new law gives Bangladesh Bank broad powers over Grameen that are similar to the central bank's authority over regular banks.
From now on Grameen must consult with the government over any major policy decision. Its 12-member board previously enjoyed broad authority to run Grameen. The legislation also specifies 60 as the retirement age for Grameen's managing director and requires the bank to be audited regularly and the audit reports submitted to parliament.
The law permits Grameen to increase its capital while the government's share of 25 percent remains unchanged. Borrowers will own 75 percent of the bank as before.
It has not increased the number of directors three appointed by the government and the rest by shareholders. The tenure of directors will be three years while previously there was no limit.
In September, the government accused Yunus of evading tax on overseas income, including from book royalties, speeches at conferences and numerous awards. Yunus says he has always acted lawfully. His supporters say the allegations are politically motivated.