Rauf Hakeem said he had been "disturbed" by recent comments from the country's defence secretary, Gotabhaya Rajapakse which warned of efforts to "promote Muslim extremism" in Sri Lanka.
"We are extremely disturbed by the specific reference to the Muslim community of Sri Lanka as possible breeding grounds of extremism within the country," Hakeem said in a statement.
"I would like to publicly contradict the assertion of the Secretary of Defence," Hakeem said in an unusual public outburst against Gotabhaya Rajapakse, who is the younger brother of President Mahinda Rajapakse.
Seventy percent of Sri Lanka's 20-million-strong population are Buddhists, while Muslims are the second-largest religious group, making up just under 10 percent.
There had been an increase in attacks against mosques and Muslim-owned business and their lifestyle since last year, heightening religious tensions on the island.
Much of the violence had been blamed on new Buddhist hardline groups allegedly drawing sup