The Mexican state-controlled oil company posted a net loss of 25.9 billion pesos in the three months to June, compared with a 16 billion peso ($1.2 billion) profit in the year-ago period.
That figure came as revenue grew by 3% to 406.1 billion pesos, or $30.6 billion.
Total production fell 1.2% to 3.68 million barrels of oil equivalent per day.
Crude oil production dropped 0.7% to 2.58 million barrels per day, while natural gas production fell 4.3% to 6.41 billion cubic feet per day.
Completion delays at the Cantarell field and drilling contracting delays contributed to the decline, Pemex said.
Low US natural gas prices were listed as a partial reason for the gas production decline.