Layton said doctors at Toronto's Princess Margaret Hospital discovered the cancer last week and he will step down temporarily while he receives treatment, the Canadian Broadcasting Corp. reported.
Layton, 61, who was first elected to Parliament in 2004 and led his party to record gains in this year's federal election, said he intends to be back on the job when lawmakers reconvene Sept. 19, the CBC said.
"I will beat this new cancer and I will be back in the House of Commons to defend the values and priorities of Canadian families," he told reporters at a news conference in Toronto.
He said an interim leader would be selected to lead the socialist NDP in his absence. He has recommended Nycole Turmel, the party's national caucus chairwoman and new member of Parliament.
Layton had been diagnosed with prostate cancer in late 2009 and revealed it in February 2010. He had hip surgery this year.
"My battle against prostate cancer is going very well. My PSA levels remain virtually undetectable," Layton said.
"However, these tests … also indicate that I have a new, non-prostate cancer that will require further treatment. So, on the advice of my doctors, I am going to focus on treatment and recovery."
Conservative Prime Minister Stephen Harper said in a statement he was "deeply saddened" by the news and offered the "heartfelt support" of his party.
"Mr. Layton is passionate about his convictions and the future of our great country," Harper said. "I would like to wish Jack a successful recovery so he can quickly return to his post.
"I salute the courage Mr. Layton continues to show in his fight against cancer, a fight that more and more Canadians are winning. We are all heartened by Jack's strength and tireless determination, which with Mr. Layton will never be in short supply."