Human rights organisations have branded it a "whitewash".
The report contradicts consistent statements from Rohingya refugees now in Bangladesh - some with gunshot wounds and severe burns - who have described massacres, rapes, looting and the burning of hundreds of villages by Myanmar's army and civilian mobs.
The results of an internal military investigation published on Monday absolved the Myanmar army of all wrongdoing during the Rohingya crisis.
A senior US State Department official later said the top diplomat would press Myanmar's powerful army chief on Wednesday to halt the violence in Rakhine and make it safe for Rohingya to return.
Myanmar's government and most of the Buddhist majority say the members of the Muslim minority are "Bengalis" who migrated illegally from Bangladesh and do not acknowledge the Rohingya as a local ethnic group even though they have lived in Myanmar, also known as Burma, for generations.
Tillerson said the United States would provide an additional $47 million in humanitarian assistance for refugees bringing the total to $87 million since the crisis erupted in August.
Amnesty International accused Myanmar of sweeping "serious violations" against the Rohingya under the carpet.
Tillerson called for a credible and impartial investigation and said those who committed abuses should be held responsible.
Trudeau urges just solution to Rohingya crisis
The human rights group called for a United Nations fact-finding mission and requested other independent investigators be given full access to Rakhine State.
The Nobel peace prize victor has failed to speak out strongly over the Rohingya's plight.
Abe and Daw Aung San Suu Kyi are in the Philippines for an Association of South East Asian Nations conference including other regional leaders.
Secretary Guterres said, "the dramatic movement of hundreds of thousands of refugees from Myanmar to Bangladesh, is a worrying escalation in a protracted tragedy and a potential source of instability in the region, and radicalization".
Canadian Prime Minister Justin Trudeau also raised the Rohingya issue in a meeting with the ASEAN leaders, including Suu Kyi, in Manila on Tuesday. Trudeau called on Tuesday for a "sustainable and just solution".
USA secretary of state Rex Tillerson said Wednesday that his country was deeply concerned by "credible reports" of atrocities committed by Myanmar's security forces and called for an independent investigation into a humanitarian crisis that has seen hundreds of thousands of Muslim Rohingya flee to Bangladesh.
The conversations in Myanmar could include consequences if the country's leaders can't formulate a "credible response" to the crisis that satisfies the global community, the official said when asked if renewed sanctions were still under consideration.
In posting on his Facebook page, Myanmar's military supremo said he had explained to Tillerson the "true situation in Rakhine", the reasons why Muslims fled, how the military was working with the government to deliver aid and the progress made for a repatriation process to be agreed with Bangladesh.