The pop singer made a joke about the former President during a live stream on her Instagram account on Saturday.
“Someone says, 'I miss your old black hair,'" Perry said, who has recently dyed her mane blonde.
"Oh, really? Do you miss Barack Obama as well? Oh, OK. Times change. Bye! See you guys later."
Some accused Perry, who has allied herself with the Black Lives Matter movement in the past and has been vocal about her support for Mr Obama, of racial insensitivity for making the joke.
"Not Katy Perry pretending to be a woke activist then making an insensitive joke comparing her hair to Obama," one critic said on Twitter.
“Katy Perry's joke was just very tasteless. What does black hair have to do with Barack Obama ... just bad,” chipped in another.
"Wow, Katy Perry. The reference to former President Obama was offensive and a poor, tasteless attempt at humour. Your privilege is showing."
Nevertheless, not everybody was angered by the comments and some argued the joke had been massively misconstrued.
Katy Perry meant she wants Obama back and can't have him same way ppl want her black hair and won't get it back ... Christ ppl lol— Wally Szczerbiak (@findingwhitney) April 30, 2017
Perry was an outspoken Hillary Clinton supporter during the last election and even went as far as designing a pair of heels in honour of the Democrat presidential candidate who lost to Donald Trump. She not only hit the campaign trail to lobby for Ms Clinton during the election but also appeared alongside her at the Unicef Snowflake Ball three weeks after the election.
A representative for Perry did not immediately respond to request for comment.