The warrant was issued by the Waigani District Court Friday according to a press statement released by acting commissioner of police, David Manning.
Whilst the release did not reveal specific allegations, Manning said he could confirm police are currently investigating.
"We have made it very clear when we came into office that we will look into all outstanding criminal cases of national significance including police shootings as well as high level corruption cases," Manning said.
Documents posted to social media appear to summon O'Neill to be questioned by police on allegations of misappropriation for payments made by National Gaming Control Board in 2012 to Yaguam Lutheran Rural Hospital in Madang.
O'Neill is currently located at the Crowne Plaza Hotel in Port Moresby, according to Manning's statement, and the acting deputy commissioner operations has requested directly to him that he be accompanied to Boroko Police Station to be processed.
In a statement released last night, the former PM said he has not seen or been issued any official arrest warrant from police.
"The fact that the acting commissioner would choose to make this announcement on social media, and not through official representation to my office, is telling me that this is a political move," he said.
"If this was a serious matter, not a political power play, a formal process would be in place that would have seen legal representation made to my office."
Corruption allegations have swirled around O'Neill over the course of his eight year tenure as prime minister.
He lost the support of his party and was replaced by current prime minister James Marape in May.
Earlier Tuesday, parliament approved legislation to establish an independent commission against corruption.
The government is determined to have an ICAC established by 2022, according to justice minister Davis Steven.