SEOUL—The fate of negotiations over North Korea’s nuclear program was cast into doubt Saturday after Pyongyang called the result of a two-day visit by U.S. Secretary of State Mike Pompeo “regrettable” and said it raised the “risk of war.”

Pyongyang’s statement offered a sharply contradictory account of the outcome of the talks after Mr. Pompeo departed the country saying that talks had been held in “good faith” and “progress” had been made on central issues.

In an early sign of the disconnect, the North Korean leader, Kim Jong Un, who met Mr. Pompeo on both previous visits to Pyongyang, did not meet the U.S. secretary of state.

The State Department declined to comment on the reaction from Pyongyang or the future of the process.

Cooperation between the two sides has been mixed since President Donald Trump met the North Korean leader in Singapore last month. At the meeting, both agreed to work toward “the complete denuclearization of the Korean Peninsula” without specifying key details.