The executive branch department determined that the phone had been compromised and should not be used any more, according to a memo circulated this week inside the White House.
The discovery raises concerns that hackers or foreign governments may have had access to data on Kelly's phone while he was secretary of Homeland Security and after he joined the West Wing.
And he has claimed that he has seldom used the compromised personal phone since taking a job in the White House. They are also uncertain of what data could have been seen or stolen. A spokesperson said Kelly uses his government phone for official communications.
Citing three White House officials, Politico said tech staff believed the phone was compromised after examining it in the summer for technical problems.
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A White House spokesman said that since joining the administration, Kelly didn't use his personal phone much and that he's used a government-issued phone for official communications and any call made from inside the White House.
The official, "who did not dispute any of Politico's reporting" on the matter, said Kelly did not have the phone anymore - but would not say where it was now.
A number of Trump's tweets have been listed as being sent from an Android phone, while others were sent from an iPhone. Trump frequently attacked Democratic presidential rival Hillary Clinton during the campaign for her own use of a private email server, saying it presented national security issues.
It's unclear how bad the hack is, or where Kelly's phone was infected with the malware.