A panel of three judges will now decide if they agree there are "reasonable grounds" to believe general Min Aung Hlaing bears criminal responsibility for the deportation and persecution of Rohingya in Myanmar and Bangladesh.
There is no set time frame for their decision but it generally takes around three months to rule on issuing an arrest warrant.
A spokesperson for Myanmar's ruling junta did not answer calls from Reuters immediately after the announcement. Reuters has requested comment from the military government by email.
The ICC prosecutor's move comes as his office faces intense political backlash from Washington, among others, over its arrest warrant for Israeli Prime Minister Benjamin Netanyahu and his former defense chief Yoav Gallant.
The prosecutor's office said in a statement that it was seeking the warrant after extensive, independent and impartial investigations. More applications for arrest warrants relating to Myanmar will follow, it said.
More than 730,000 Rohingya Muslims fled to Bangladesh during the campaign which U.N. investigators said was carried out with "genocidal intent".
Buddhist majority Myanmar denies accusations of genocide and has always maintained it does not target civilians, saying it carried out military operations against terrorists.
Myanmar is not a member of the treaty-based ICC, but in 2018 and 2019 rulings judges said the court had jurisdiction over alleged cross-border crimes that partially took place in neighbouring ICC member Bangladesh, and said prosecutors could open a formal investigation.
"This is the first application for an arrest warrant against a high-level Myanmar government official that my Office is filing. More will follow," the ICC prosecutor's statement said.
The ICC has been investigating crimes against the Rohingya for nearly five years. Its investigation has not only been hampered by a lack of access to the country but also because Myanmar has been in turmoil since the military ousted an elected government led by Nobel laureate Aung San Suu Kyi in 2021, sparking a resistance movement that began as peaceful protests and later evolved into an armed rebellion on multiple fronts.
Investigators drew upon a wide variety of evidence from witness testimonies, including from a number of insider witnesses, documentary evidence and authenticated scientific, photographic and video materials, they said.
"The ICC prosecutor’s decision to seek a warrant against Sr. Gen. Min Aung Hlaing comes amid renewed atrocities against Rohingya civilians that echo those suffered seven years ago," Maria Elena Vignoli, senior international justice counsel at Human Rights Watch said.
"The ICC’s action is an important step toward breaking the cycle of abuses and impunity that has long been a key factor in fuelling the military’s mass violations."
