"We have already let the world know that we don't have Rohingya in our country," army chief Min Aung Hlaing said in a speech marking Myanmar's armed forces day.
"Bengalis in Rakhine state are not Myanmar citizens and they are just people who come and stay in the country," Hlaing added.
Myanmar is now under civilian leadership but its powerful military, which ruled the country until recently and built up a notorious reputation for rights abuses, still uses the armed forces day to flex its muscle.
Rohingya Muslims, stripped of their citizenship in 1982, are often referred to as "illegal" immigrants by Myanmar's leaders. About 1.1 million Rohingya are denied citizenship and their movement is severely restricted, with tens of thousands confined to dire camps since violence drove them from their homes in 2012.
Hlaing's speech came just one day after the government rejected a decision by the United Nations rights council's to send a fact-finding mission to Myanmar to investigate allegations of rape and murder by security forces against Rohingya.
On Friday, the UN Human Rights Council agreed to "urgently" dispatch an independent, international mission to investigate the findings of a February UN report that alleged that the security operations in Rakhine state involved mass rapes and killings.
Myanmar's civilian government has rebuffed the probe, saying it "would do more to inflame, rather than resolve the issues at this time".
Tens of thousands of people have fled Myanmar’s Rakhine state since the military began a security operation last October in response to what it says was an attack by Rohingya armed men on border posts, in which nice police officers were killed.
"The terrorist attacks which took place in October 2016 resulted in the political interferences," Hlaing said on Monday, defending the government's operation.
"We have a duty to do what we should do according to the law and we also have a duty to protect our sovereignty when it is harmed by political, religious and racial problems in the country," he added.
The UN rights body has stopped short of launching a Commission of Inquiry - the world body's highest level of investigation, which Myanmar has been staunchly opposed.
The country's leader, Aung San Suu Kyi, a nobel peace laureate, launched a domestic inquiry into possible crimes in Rakhine state and appointed former UN chief Kofi Annan to head a commission responsible for healing long-simmering divisions between Buddhists and Muslims.
Earlier this month, that commission said that Myanmar should close the camps where more than 120,000 Rohingya have languished since they were driven from their homes after a wave of inter-religious violence engulfed parts of Rakhine state in 2012.
Suu Kyi's office welcomed the report and said it would implement a "large majority" of its recommendations, while "a few will be contingent upon the situation on the ground".