"My Muslim brothers in Bangladesh, I invite you to confront this crusade onslaught against Islam," Zawahiri said in an audio message released by a jihadi website.
"Bangladesh is the victim of a conspiracy in which the agents of India, the corrupt leadership of Pakistan Army and treacherous power-hungry politicians of Bangladesh and Pakistan are all involved," he was quoted as saying in reports on Bangladeshi news websites.
The audio message claimed the onslaught was being orchestrated by "leading criminals in the subcontinent and the West".
His tirade was apparently provoked by Bangladesh's war crimes trials, in which senior leaders of fundamentalist Jamaat-e-Islami are implicated, bdnews24 portal reported.
Jamaat leader Abdul Quader Molla has already been hanged for atrocities duing the 1971 war of independence and several others are facing death and life sentences.