Consumer price inflation slowed to 4.51 percent from 4.55 percent in April, the agency said. However, the rate exceeded the 4.43 percent forecast of analysts in a Reuters poll.
The annual rate was the lowest since a reading of 3.36 percent in December 2016, official data showed.
Annual inflation accelerated sharply in 2017 when government-set gasoline prices began being phased out, bumping up the cost of fuel in Latin America's No. 2 economy.
Compared to the previous month, consumer prices fell 0.16 percent, less than the 0.23 percent drop forecast in the poll.
The core index, which strips out some volatile food and energy prices, rose 0.26 percent during the month.
The Mexican central bank targets inflation of around 3 percent, and in February it hiked interest rates to 7.50 percent to contain inflation risks. The bank's key lending rate is at its highest level since early 2009.