Prime Minister Enrico Letta said the remark by Senator Roberto Calderoli on Saturday was "unacceptable".
"I love animals… but when I see pictures of Kyenge, I cannot help thinking of similarities with an orangutan," he was quoted as saying at a party meeting in the northern city of Treviglio.
The remark went viral in social media, sparking widespread denunciation.
Letta said in a statement on Sunday: "The words reported today in the press attributed to Senator Calderoli regarding Cecile Kyenge are unacceptable and go beyond all limits.
Khalid Chaouki and Gianni Cuperlo, two lawmakers from the centre-left Democratic Party, demanded the resignation of Calderoni, who is deputy speaker of the Senate.
"The remarks addressed to Minister Kyenge are not worthy of a man who represents our institutions," Cuperlo said.
Calderoli is famous for his provocative comments and actions. In 2006, he was forced to resign from the government of then prime minister Silvio Berlusconi after wearing a T-shirt printed with cartoons mocking the prophet Mohammed.
Since the Democratic Republic of Congo-born Kyenge took up her post as integration minister earlier this year she has faced numerous expressions of hostility from the Northern League, which is allied with Berlusconi's centre-right People of Freedom party but is now in opposition.
She has been the subject of verbal slurs and death threats posted on racist social media sites and even on her own Facebook page.